{"gene":"SYVN1","run_date":"2026-06-14T07:33:11","timeline":{"discoveries":[{"year":2001,"finding":"Der3/Hrd1p (SYVN1) is a six-transmembrane ER membrane protein with cytoplasmic N- and C-termini; its RING-H2 finger domain is required for ubiquitination of misfolded ER proteins, and it directly binds the E2 ubiquitin-conjugating enzyme Ubc7p through this RING domain, establishing it as the E3 ubiquitin ligase of the ERAD pathway.","method":"Membrane topology mapping, in vitro ubiquitination assay, Ubc7p binding assay, in vivo RING-finger mutant analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted in vitro ubiquitination, topology mapping, and mutational analysis in a single rigorous study","pmids":["11139575"],"is_preprint":false},{"year":1999,"finding":"The RING-H2 finger motif of Der3/Hrd1p is essential for ERAD function; a C399S point mutation abolishes degradation of both soluble and integral membrane misfolded ER proteins and acts as a dominant negative, while Hrd3p overexpression suppresses this dominant effect, suggesting competition for Hrd3p interaction.","method":"Site-directed mutagenesis, in vivo degradation assay, dominant-allele analysis, genetic suppression","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1 / Strong — mutagenesis plus genetic epistasis with multiple orthogonal readouts","pmids":["10218484"],"is_preprint":false},{"year":2008,"finding":"OS-9 and XTP3-B (Erlectin) are ER-resident glycoproteins that bind ERAD substrates (mutant α1-antitrypsin) and, through the SEL1L adaptor, deliver them to the HRD1 ubiquitin ligase complex; OS-9 also associates with the ER chaperone GRP94. The MRH domains of OS-9/XTP3-B are required for SEL1L interaction but not for substrate binding.","method":"Co-immunoprecipitation, siRNA knockdown with degradation assay, domain mutagenesis","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, domain mutagenesis, functional knockdown, replicated across two lectin paralogs","pmids":["18264092"],"is_preprint":false},{"year":2016,"finding":"Autoubiquitination of Hrd1 within its RING-finger domain triggers retrotranslocation of misfolded luminal protein domains across the ER membrane in a reconstituted proteoliposome system; substrate ubiquitination is a subsequent event and the Cdc48 ATPase is not required for the retrotranslocation step itself.","method":"In vitro reconstitution with purified S. cerevisiae proteins in proteoliposomes, RING-finger lysine mutagenesis, in vivo ERAD assay","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — full biochemical reconstitution with purified components plus mutagenesis and in vivo validation","pmids":["27321670"],"is_preprint":false},{"year":2017,"finding":"Cryo-EM structure of S. cerevisiae Hrd1 in complex with Hrd3 shows Hrd1 forms a dimer in the membrane; each Hrd1 molecule has eight transmembrane segments with an aqueous cavity extending from the cytosol nearly to the ER lumen and a lateral gate, consistent with a retrotranslocation channel.","method":"Cryo-electron microscopy structural determination","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure with near-atomic resolution providing direct mechanistic insight","pmids":["28682307"],"is_preprint":false},{"year":2020,"finding":"Cryo-EM structure of the active five-subunit Hrd1 complex (Hrd1, Hrd3, Der1, Usa1, Yos9) reveals Hrd3 and Yos9 jointly create a luminal substrate-binding site for glycosylated substrates; Hrd1 and the rhomboid-like Der1 form two 'half-channels' with opposing cavities and lateral gates in a thinned membrane region, explaining how a polypeptide loop moves through the membrane during ERAD-L.","method":"Cryo-EM of two subcomplexes, crosslinking, molecular dynamics simulation","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure combined with crosslinking and MD simulation, multiple orthogonal methods","pmids":["32327568"],"is_preprint":false},{"year":2020,"finding":"Purified Hrd1 incorporated into model membranes forms a pore whose opening is triggered by autoubiquitination; substrate binding increases pore size and activity; deubiquitination closes the pore. Two substrate-binding sites were identified: a low-affinity luminal site and a high-affinity cytoplasmic site formed after autoubiquitination of specific RING-domain lysines.","method":"Reconstitution of purified Hrd1 in model membranes, electrophysiology/pore assay, site-specific mutagenesis of RING-domain lysines","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct in vitro pore reconstitution with purified protein plus mutagenesis","pmids":["32094691"],"is_preprint":false},{"year":2019,"finding":"Hrd1 autoubiquitination is counteracted by the deubiquitinating enzyme Ubp1, which requires its N-terminal transmembrane segment for activity toward Hrd1. Hrd3 acts as a brake on autoubiquitination, while Usa1 attenuates Ubp1 deubiquitination through its UBL domain, establishing a cycle of autoubiquitination/deubiquitination that gates the Hrd1 retrotranslocation channel.","method":"Genetic and biochemical analysis in S. cerevisiae, ubiquitination/deubiquitination assays, domain mutagenesis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal genetic and biochemical approaches identifying writer/eraser/regulator of Hrd1 autoubiquitination","pmids":["31713515"],"is_preprint":false},{"year":2022,"finding":"Site-specific disulfide crosslinking in live S. cerevisiae cells maps the path of a glycosylated ERAD substrate through the Hrd1 complex: the substrate contacts a groove in Hrd3 and the lectin domain of Yos9 on the luminal side, inserts a loop into the membrane with one side interacting with the Der1 lateral gate and the other with the Hrd1 lateral gate. Hrd1 autoubiquitination is required to disassemble inactive Hrd1 dimers into active monomers.","method":"Site-specific disulfide crosslinking in live cells, cryo-EM structure integration","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — site-specific crosslinking in living cells with structural integration, multiple interaction points mapped","pmids":["35970394"],"is_preprint":false},{"year":2010,"finding":"SEL1L protein stability is critically dependent on HRD1: SEL1L is rapidly degraded when HRD1 is absent, and HRD1 co-expression stabilizes SEL1L. The endogenous HRD1-SEL1L complex (Complex I) associates with Derlin-1/2, VIMP, Herp, and OS-9, while a smaller transiently expressed complex (Complex II) lacks Derlin-1/2, VIMP, and Herp but still supports retrotranslocation.","method":"siRNA knockdown, co-immunoprecipitation, size fractionation, degradation assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods, reciprocal Co-IP, functional knockdown with defined substrates","pmids":["21454652"],"is_preprint":false},{"year":2010,"finding":"Disposal of soluble ERAD-L substrates (ERAD-LS) in mammalian cells is strictly dependent on HRD1, SEL1L, and either OS-9 or XTP3-B; tethering the same substrate to the membrane (ERAD-LM) renders these factors dispensable, revealing a distinct pathway organization from yeast.","method":"siRNA knockdown with pulse-chase degradation assays, genetic epistasis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic genetic epistasis with multiple substrates and multiple ERAD components","pmids":["20100910"],"is_preprint":false},{"year":2024,"finding":"SEL1L-HRD1 interaction is required to form a functional ERAD complex: SEL1L is needed to recruit the E2 enzyme UBE2J1 and DERLIN to HRD1. A disease-causing SEL1L variant (p.Ser658Pro) reduces SEL1L stability and attenuates the SEL1L-HRD1 interaction via electrostatic repulsion between SEL1L F668 and HRD1 Y30, impairing ERAD.","method":"Biochemical analysis, proteomic interactome screens, mutagenesis, mouse model with pathogenic variant","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — proteomics, mutagenesis, and mouse pathology, multiple orthogonal methods","pmids":["38365914"],"is_preprint":false},{"year":2011,"finding":"HRD1 acts together with the E2 ubiquitin-conjugating enzyme UBE2J1 to ubiquitinate and dislocate misfolded MHC class I heavy chains from the ER. HRD1, UBE2J1, non-β2m-bound MHC I heavy chains, Derlin-1, and p97 form a complex. HRD1 discriminates misfolded MHC I from properly assembled heterotrimers.","method":"siRNA functional screen, Co-immunoprecipitation, ubiquitination assay, dislocation assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — functional siRNA screen, Co-IP complex characterization, ubiquitination assay, multiple orthogonal methods","pmids":["21245296"],"is_preprint":false},{"year":2014,"finding":"Hrd1 ubiquitinates Nrf2 and targets it for proteasomal degradation independently of the canonical Keap1 pathway. In cirrhotic livers, XBP1 transcriptionally up-regulates Hrd1, which then ubiquitinates Nrf2, suppressing the antioxidant response. Hrd1 conditional knockout mice show elevated Nrf2 levels.","method":"Hrd1 conditional knockout mouse model, ubiquitination assay, liver cirrhosis patient tissue analysis, XBP1-Hrd1 transcriptional pathway analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional knockout plus in vitro ubiquitination assay, replicated in human tissue and mouse model","pmids":["24636985"],"is_preprint":false},{"year":2014,"finding":"Hrd1 catalyzes ubiquitination and degradation of the transcriptional suppressor BLIMP1 in dendritic cells, thereby promoting MHC-II expression. Hrd1-null DCs fail to prime CD4+ T cells. Hrd1 expression is induced by TLR stimulation.","method":"Conditional Hrd1 knockout in DCs, ubiquitination assay, T cell priming assay","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — tissue-specific knockout with defined cellular phenotype, ubiquitination assay","pmids":["25366967"],"is_preprint":false},{"year":2016,"finding":"Hrd1 ubiquitinates and degrades the CDK inhibitor p27(kip1) to promote T cell proliferation; genetic deletion of Hrd1 in T cells impairs proliferation and IL-2 production, and deletion of p27(kip1) in Hrd1-null T cells rescues proliferative capacity but not cytokine production.","method":"Conditional Hrd1 knockout mouse, genetic rescue (p27 deletion), ubiquitination assay, T cell functional assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional knockout plus genetic epistasis with p27 deletion, multiple phenotypic readouts","pmids":["27417417"],"is_preprint":false},{"year":2016,"finding":"Hrd1 ubiquitinates and degrades the death receptor Fas/CD95 in B cells, protecting them from activation-induced cell death. Hrd1-null B cells exhibit elevated Fas expression during activation and undergo Fas-mediated apoptosis; Fas mutation in Hrd1 KO mice abrogates the B-cell AICD increase.","method":"Conditional Hrd1 knockout mouse, genetic rescue (Fas mutation), ubiquitination assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional knockout with genetic epistasis via Fas mutation, ubiquitination assay","pmids":["27573825"],"is_preprint":false},{"year":2016,"finding":"Sel1L-Hrd1 ERAD selectively recognizes and targets the pre-B cell receptor (pre-BCR) for proteasomal degradation in a BiP-dependent manner; loss of Sel1L-Hrd1 causes pre-BCR accumulation intracellularly and at the cell surface, leading to persistent pre-BCR signaling and developmental block at the large-to-small pre-B cell transition.","method":"Conditional Sel1L knockout in B cell precursors, pre-BCR accumulation analysis, signaling assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional knockout with defined developmental block and mechanistic pathway placement","pmids":["27568564"],"is_preprint":false},{"year":2020,"finding":"Sel1L-Hrd1 ERAD controls β cell identity by mediating the degradation of TGF-β receptor 1; Sel1L deficiency leads to loss of β cell identity (not apoptosis) that can be rescued by inhibition of TGF-β signaling, as demonstrated by single-cell RNA-seq and TGF-β receptor 1 protein accumulation.","method":"β cell-specific Sel1L conditional knockout, single-cell RNA-seq, TGF-β receptor 1 degradation assay, TGF-β pathway inhibition rescue","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — tissue-specific knockout with scRNA-seq, defined substrate, and pharmacological rescue","pmids":["32182217"],"is_preprint":false},{"year":2018,"finding":"The Sel1L-Hrd1 ERAD complex controls FGF21 transcription by ubiquitinating and degrading the ER-tethered transcription factor CREBH; liver-specific Sel1L deletion elevates CREBH nuclear abundance and markedly increases circulating FGF21, establishing a hepatic ERAD-CREBH-FGF21 metabolic axis.","method":"Liver-specific Sel1L knockout mouse, CREBH ubiquitination assay, FGF21 measurement","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — tissue-specific knockout with defined substrate ubiquitination assay, replicated in two papers (PMID:30389665 and 30389664)","pmids":["30389665","30389664"],"is_preprint":false},{"year":2018,"finding":"HRD1 catalyzes polyubiquitin conjugation onto CREBH at lysine K294, targeting it for proteasomal degradation in the postprandial state to downregulate FGF21 expression in liver.","method":"Liver-specific HRD1 knockout mouse, CREBH ubiquitination site mapping (K294), refeeding experiments","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — specific ubiquitination site identified, tissue-specific knockout, in vivo metabolic phenotyping","pmids":["30389664"],"is_preprint":false},{"year":2023,"finding":"The SEL1L-HRD1 ERAD complex ubiquitinates nascent STING protein and targets it for proteasomal degradation in the basal state, limiting the pool of activatable STING and thus suppressing innate immune signaling; SEL1L or HRD1 deficiency in macrophages amplifies STING-dependent antiviral and antitumor immunity.","method":"Conditional knockout in macrophages, ubiquitination assay, STING signaling assays, viral infection and tumor models","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional knockout with defined substrate, ubiquitination assay, functional immune phenotype, multiple disease models","pmids":["37142791"],"is_preprint":false},{"year":2006,"finding":"HRD1 interacts with Parkin-associated endothelin receptor-like receptor (Pael-R) through its proline-rich region, promotes Pael-R ubiquitination and degradation via the proteasome, prevents Pael-R-induced ER stress and neuronal death; ATF6 overexpression induces HRD1 and accelerates Pael-R degradation in an HRD1-dependent manner.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, ATF6 overexpression, neuronal cell death assay","journal":"Journal of neurochemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, ubiquitination assay, siRNA rescue, mechanistic pathway placement","pmids":["17059562"],"is_preprint":false},{"year":2010,"finding":"HRD1 promotes ubiquitination and degradation of amyloid precursor protein (APP) through its proline-rich region interaction; suppression of HRD1 by siRNA causes APP accumulation, increased Aβ production, and ER stress; ATF6/XBP1-induced HRD1 upregulation enhances APP degradation and reduces Aβ production.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, APP and Aβ measurement","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, ubiquitination assay, siRNA, multiple readouts","pmids":["20237263"],"is_preprint":false},{"year":2006,"finding":"Hrd1 interacts with and ubiquitinates polyglutamine-expanded huntingtin N-terminal fragment (httN) in a RING-finger-dependent manner; Hrd1 recruits httN to the ER and co-localizes with juxtanuclear httN aggregates; Hrd1-mediated httN degradation is p97/VCP-dependent but Ufd1/Npl4-independent; expanded polyQ tracts are preferred substrates.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, subcellular fractionation, confocal microscopy","journal":"Experimental cell research","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, ubiquitination, siRNA, imaging, multiple orthogonal methods","pmids":["17141218"],"is_preprint":false},{"year":2009,"finding":"Both Hrd1 and gp78 bind cholera toxin CTA1 and protein disulfide isomerase (PDI); dominant-negative Hrd1 or gp78 and Ube2g2 mutants decrease CTA1 retrotranslocation; CT association with Hrd1/gp78 is blocked by dominant-negative Derlin-1, suggesting a sequential handoff from Derlin-1 to Hrd1/gp78 on the ER membrane.","method":"Binding studies (Co-immunoprecipitation), dominant-negative mutant expression, retrotranslocation assay, siRNA knockdown","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional dominant-negative approach, single lab","pmids":["19864457"],"is_preprint":false},{"year":2013,"finding":"Derlin-2, but not Derlin-1 or Derlin-3, is an essential functional partner for HRD1-mediated ERAD of sonic hedgehog (SHH) and NHK substrates; without Derlin-2, HRD1 homo-oligomerization and substrate targeting proceed normally but substrates are trapped in the ER lumen, suggesting Derlin-2 regulates substrate movement through the HRD1 retrotranslocon.","method":"siRNA knockdown of individual Derlins, ERAD substrate degradation assay, retrotranslocation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic siRNA knockdown of three Derlins with functional retrotranslocation readout, multiple substrates tested","pmids":["23867461"],"is_preprint":false},{"year":2013,"finding":"HERP proteins (HERP1/HERP2) are required for HRD1-mediated ERAD; they recruit DERL2 to the HRD1-SEL1L complex, and loss of HERPs traps substrates in the ER lumen and attenuates their ubiquitination. HERP2 is constitutively expressed whereas HERP1 is ER stress-inducible. The UBL domain of HERP1 has an additional function independent of DERL2 recruitment.","method":"siRNA knockdown, Co-immunoprecipitation, ERAD substrate degradation/retrotranslocation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple HERP paralogs tested, Co-IP, functional retrotranslocation readout","pmids":["24366871"],"is_preprint":false},{"year":2014,"finding":"Herp localizes to the ER quality control compartment (ERQC) and recruits HRD1 to this compartment; Herp is required for HRD1-mediated ubiquitination of ERAD substrates presented by OS-9 lectin at the ERQC.","method":"Confocal microscopy/live imaging, Co-immunoprecipitation, siRNA knockdown with ERAD substrate assay","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — imaging plus Co-IP and functional assay, single lab","pmids":["24478453"],"is_preprint":false},{"year":2010,"finding":"Herp regulates Hrd1-mediated ubiquitylation through its ubiquitin-like (UBL) domain; the UBL domain is required for efficient ubiquitylation of the NHK ERAD substrate and for NHK degradation. Herp undergoes rapid turnover at Hrd1 complexes with multiple copies of Hrd1 per complex.","method":"Co-immunoprecipitation, UBL domain mutagenesis, ubiquitylation assay with NHK substrate","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mutagenesis plus Co-IP and functional ubiquitylation assay, single lab","pmids":["21149444"],"is_preprint":false},{"year":2017,"finding":"Affinity-tagged endogenous Hrd1 in HEK293 cells forms two distinct high-molecular-mass complexes with different interacting proteins and variable stoichiometries, indicating heterogeneity in functional Hrd1 ERAD units; complex composition is strongly influenced by Hrd1 expression levels.","method":"Genome-edited endogenous tandem affinity tag, size-exclusion chromatography, immunodepletion, absolute quantification mass spectrometry","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — endogenous tagging by genome editing plus quantitative MS, multiple biochemical fractionation methods","pmids":["28411238"],"is_preprint":false},{"year":2018,"finding":"During ER stress, HRD1 associates with the Sec61α translocon and Derlin-1 to form a large pre-emptive quality control (ERpQC) complex; ERpQC substrates are captured by the C-terminal region of Derlin-1 and ubiquitinated by HRD1 prior to cytosolic degradation.","method":"Co-immunoprecipitation, ubiquitination assay, ER stress induction","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of trimeric complex plus ubiquitination assay, single lab","pmids":["29743537"],"is_preprint":false},{"year":2016,"finding":"Grp94 uses its middle domain to interact with GABAA receptor α1 subunits in the ER lumen; OS-9 acts downstream of Grp94 to recognize misfolded α1 subunits in a glycan-dependent manner, delivering them to Hrd1-mediated ubiquitination and VCP-mediated extraction.","method":"Co-immunoprecipitation, domain mutagenesis, Grp94 inhibition, ERAD substrate assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, domain mapping, pharmacological inhibition, single lab","pmids":["26945068"],"is_preprint":false},{"year":2007,"finding":"ER stress-induced transcription of HRD1 is mediated by the IRE1-XBP1 pathway, while SEL1 induction is mediated by the ATF6-dependent pathway, revealing differential regulation of these ERAD components by distinct UPR branches.","method":"IRE1/ATF6 inhibition, XBP1 overexpression, promoter-linked induction analysis","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pathway inhibition and transcription factor overexpression, mechanistic pathway placement, single lab","pmids":["17967421"],"is_preprint":false},{"year":2016,"finding":"USP19, an ER-anchored deubiquitinating enzyme, stabilizes HRD1 by removing K48-linked ubiquitin chains from HRD1, rescuing it from proteasomal degradation; altered USP19 expression affects steady-state HRD1 levels.","method":"Co-immunoprecipitation, ubiquitination assay, USP19 overexpression/knockdown","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, gain/loss-of-function, single lab","pmids":["27827840"],"is_preprint":false},{"year":2023,"finding":"HRD1 is UFMylated at Lys610 by UFL1 and interacts with UFMylation components UFL1 and DDRGK1; UFL1 depletion increases HRD1 stability and reduces its ubiquitination. Mutation of HRD1 K610R impairs its ability to degrade misfolded proteins. During ER stress, UFMylation and ubiquitination of HRD1 are progressively inhibited.","method":"Co-immunoprecipitation, UFMylation assay, site-directed mutagenesis (K610R), siRNA knockdown, ERAD substrate degradation assay","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — novel PTM identified with mutagenesis and functional ERAD readout, single lab","pmids":["37795761"],"is_preprint":false},{"year":2019,"finding":"ER-localized Hrd1 directly interacts with the deubiquitinating enzyme Usp15 and inactivates its deubiquitinating activity toward IκBα (without degrading Usp15), resulting in enhanced IκBα ubiquitination and excessive NF-κB activation during TLR4-triggered bacterial infection; Hrd1 deficiency in macrophages protects mice from LPS-induced septic shock.","method":"Co-immunoprecipitation, deubiquitinase activity assay, Hrd1 knockout macrophages, septic shock mouse model, rescue with Usp15 knockdown","journal":"Nature microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, enzymatic activity assay, in vivo knockout model with rescue, multiple orthogonal methods","pmids":["31477895"],"is_preprint":false},{"year":2019,"finding":"Hrd1 suppresses ER stress-induced IRE1α-p38 MAPK signaling in regulatory T cells (Tregs); genetic deletion of Hrd1 in Tregs elevates ER stress-responsive genes and IRE1α/p38 activation, destabilizing FoxP3 expression; pharmacological suppression of IRE1α kinase (but not endonuclease) activity rescues Hrd1-null Treg stability.","method":"Treg-specific Hrd1 conditional knockout, IRE1α kinase/endonuclease pharmacological inhibition, FoxP3 stability assay, multi-organ inflammation phenotype","journal":"JCI insight","confidence":"High","confidence_rationale":"Tier 2 / Strong — cell type-specific conditional knockout, pharmacological dissection of IRE1α activities, defined FoxP3 stability readout","pmids":["30843874"],"is_preprint":false},{"year":2021,"finding":"HRD1 ubiquitinates and degrades METTL14; in ER stress, accumulation of unfolded proteins competes with HRD1 to block METTL14 ubiquitination, allowing METTL14 accumulation to promote m6A modification of CHOP mRNA and reduce its translation, thereby shifting UPR toward stress adaptation over apoptosis.","method":"HRD1 ERAD machinery competition assay, METTL14 ubiquitination assay, m6A modification analysis, liver-specific METTL14 knockout","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — ubiquitination assay, tissue-specific knockout, mechanistic pathway connecting ERAD to mRNA modification","pmids":["34847358"],"is_preprint":false},{"year":2021,"finding":"SYVN1/HRD1 directly interacts with GSDMD and mediates K27-linked polyubiquitination of GSDMD at K203 and K204 residues, promoting GSDMD-induced pyroptotic cell death; SYVN1 deficiency inhibits pyroptosis.","method":"Co-immunoprecipitation, in vitro ubiquitination assay with specific ubiquitin linkage analysis, site-directed mutagenesis of GSDMD lysines, LDH/PI uptake cell death assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination site mutagenesis, functional pyroptosis assay, single lab","pmids":["35115505"],"is_preprint":false},{"year":2017,"finding":"SYVN1/HRD1 enhances degradation of the ATZ (SERPINA1 E342K) variant through SQSTM1/p62-dependent selective autophagy; SYVN1 mediates K48-linked polyubiquitination of ATZ, which is recognized by the UBA domain of SQSTM1, coupling ubiquitinated ATZ to the lysosome; autophagy inhibition attenuates SYVN1-mediated ATZ clearance.","method":"Ubiquitination assay (K48 linkage specific), autophagy inhibition/induction, Atg5 knockout cells, SQSTM1 UBA domain analysis, Co-immunoprecipitation","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 / Strong — specific ubiquitin linkage analysis, genetic autophagy disruption (Atg5 KO), domain mapping, multiple orthogonal methods","pmids":["28121484"],"is_preprint":false},{"year":2017,"finding":"Hrd1 interacts with tau and promotes proteasomal degradation of both total tau and phosphorylated tau through its E3 ubiquitin ligase activity; proteasome inhibition increases Hrd1-mediated tau ubiquitination; Hrd1 overexpression alleviates tau cytotoxicity.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, proteasome inhibitor treatment, cell viability assay","journal":"Current molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, siRNA, single lab","pmids":["22280354"],"is_preprint":false},{"year":2017,"finding":"Hrd1 interacts with optineurin (OPTN) and promotes its proteasomal degradation and aggresome formation at the MTOC; Hrd1 overexpression increases OPTN degradation and aggresome formation, while Hrd1 knockdown stabilizes OPTN and inhibits aggresome formation; this applies to both WT and ALS/POAG mutant OPTN.","method":"Co-immunoprecipitation, siRNA knockdown, proteasome assay, confocal microscopy of aggresome formation","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, siRNA, imaging, single lab","pmids":["28334804"],"is_preprint":false},{"year":2016,"finding":"SYVN1 (HRD1), NEDD8, and FBXO2 each contribute to ubiquitin-mediated proteasomal degradation of ΔF508-CFTR in human cystic fibrosis airway epithelia; knockdown of SYVN1, NEDD8, or FBXO2 partially restores ΔF508-CFTR-mediated Cl- transport; SYVN1 and FBXO2 represent two distinct multiprotein complexes targeting ΔF508-CFTR.","method":"siRNA knockdown in primary human airway epithelia, functional CFTR Cl- transport assay, CFTR maturation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional siRNA screen in primary human cells, two orthogonal CFTR assays, single lab","pmids":["27756846"],"is_preprint":false},{"year":2009,"finding":"Silencing of Hrd1 leads to stabilization of gp78 and a decline in gp78 ubiquitination, thereby enhancing CFTRΔf508 degradation; endogenous gp78 co-immunoprecipitates with Hrd1, and Hrd1 acts as an E3 for gp78, negatively regulating CFTRΔf508 degradation.","method":"siRNA knockdown, Co-immunoprecipitation, ubiquitination assay, cycloheximide chase","journal":"The international journal of biochemistry & cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination, siRNA, single lab","pmids":["19828134"],"is_preprint":false},{"year":2018,"finding":"HRD1 interacts with and ubiquitinates multiple metabolic enzymes including ENTPD5, CPT2, RMND1, and HSD17B4 in the liver; liver-specific HRD1 deletion elevates these proteins and hyperactivates AMPK and AKT pathways, reprogramming hepatic metabolic gene expression to suppress glycogenesis/lipogenesis and upregulate glycolysis/fatty acid oxidation.","method":"Liver-specific HRD1 knockout, proteomic interactome analysis, ubiquitination assay, genome-wide mRNA sequencing, metabolic phenotyping","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — tissue-specific knockout, proteomics interactome, functional metabolic phenotyping, multiple substrates validated","pmids":["30201971"],"is_preprint":false},{"year":2020,"finding":"HRD1 interacts with and ubiquitinates MafA in diabetic β-cells, leading to its cytoplasmic accumulation and proteasomal degradation; HRD1 overexpression triggers impaired insulin secretion via MafA loss, while HRD1 knockdown improves glucose control in diabetic models.","method":"Proteomic analysis, Co-immunoprecipitation, ubiquitination assay, β cell-specific HRD1 overexpression and knockdown mouse models","journal":"Diabetes","confidence":"High","confidence_rationale":"Tier 2 / Strong — proteomics substrate identification, Co-IP, ubiquitination assay, in vivo mouse model","pmids":["32086291"],"is_preprint":false},{"year":2017,"finding":"HRD1 interacts with eIF2α and promotes its ubiquitylation and proteasomal degradation; HRD1 overexpression decreases phosphorylated eIF2α levels and inhibits apoptosis in renal tubular cells exposed to palmitic acid or high glucose; the protective effect of HRD1 is blunted by eIF2α overexpression.","method":"Co-immunoprecipitation, ubiquitination assay, HRD1 overexpression/knockdown, apoptosis assay","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, rescue experiment, single lab","pmids":["29233968"],"is_preprint":false},{"year":2015,"finding":"HRD1 interacts with IGF-1R and promotes its ubiquitination and proteasomal degradation in breast cancer cells; NF-κB/p65 binds the HRD1 promoter and inhibits HRD1 expression, explaining IL-6-induced HRD1 downregulation; HRD1 overexpression inhibits breast cancer growth and invasion in vitro and in vivo.","method":"Co-immunoprecipitation, ubiquitination assay, promoter binding analysis, overexpression in vitro/in vivo","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, promoter analysis, single lab","pmids":["26536657"],"is_preprint":false},{"year":2020,"finding":"HRD1 interacts with and ubiquitinates SIRT2, promoting its proteasomal degradation; HRD1 deficiency induces SIRT2 upregulation and inhibits lung cancer cell growth and tumor formation both in vitro and in vivo.","method":"Co-immunoprecipitation, ubiquitination assay, HRD1 knockdown/overexpression, tumor xenograft model","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, in vivo model, single lab","pmids":["31932479"],"is_preprint":false},{"year":2021,"finding":"HRD1 interacts with and ubiquitinates PFKP, targeting it for proteasomal degradation; HRD1-mediated PFKP degradation reduces aerobic glycolysis (Warburg effect) and inhibits breast cancer cell proliferation and invasion.","method":"Mass spectrometry HRD1 interactome, Co-immunoprecipitation, ubiquitylation assay, in vitro/in vivo tumor models","journal":"Cell communication and signaling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS interactome, Co-IP, ubiquitination assay, in vivo xenograft, single lab","pmids":["33588886"],"is_preprint":false},{"year":2020,"finding":"HRD1 interacts with CPT2 and mediates K48-linked ubiquitination of CPT2, stabilizing (not degrading) it; HRD1-mediated CPT2 stabilization inhibits fatty acid oxidation and TNBC cell proliferation under glutamine-deficient conditions.","method":"Co-immunoprecipitation, ubiquitination assay with K48 linkage analysis, CPT2 knockdown rescue, in vivo xenograft","journal":"Molecular oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, specific ubiquitin linkage analysis, functional rescue, single lab","pmids":["33207079"],"is_preprint":false},{"year":2020,"finding":"Hrd1 interacts with and ubiquitinates LOX-1, promoting its proteasomal degradation in endothelial cells; KLF2 transcription factor binds the HRD1 promoter and positively regulates HRD1 expression; loss of HRD1 causes LOX-1 accumulation and endothelial apoptosis.","method":"Co-immunoprecipitation, ubiquitination assay, KLF2 promoter binding analysis, LOX-1 knockdown rescue","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination, promoter analysis, single lab","pmids":["32308114"],"is_preprint":false},{"year":2020,"finding":"Hrd1 interacts with and ubiquitinates Acly (ATP citrate lyase), reducing its protein level and suppressing acetyl-CoA production and lipogenesis in hepatocytes; Hrd1 overexpression in db/db mice ameliorates hepatic steatosis and improves insulin sensitivity.","method":"Co-IP-based mass spectrometry, Co-immunoprecipitation, ubiquitination assay, adenovirus overexpression in db/db mice","journal":"Metabolism: clinical and experimental","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS interactome, Co-IP, ubiquitination, in vivo mouse model, single lab","pmids":["32888949"],"is_preprint":false},{"year":2018,"finding":"HRD1 interacts with PTEN and promotes its ubiquitination and proteasomal degradation in hepatocellular carcinoma; HRD1 suppression inhibits HCC growth, migration, and invasion.","method":"Proteomic approach, Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, in vitro/in vivo tumor models","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination, in vivo model, single lab","pmids":["29958993"],"is_preprint":false},{"year":2023,"finding":"SYVN1/HRD1 interacts with and ubiquitinates HMGB1, promoting its degradation; SYVN1-mediated HMGB1 degradation activates the NRF2/HO-1 pathway and inhibits ferroptosis in spinal cord neurons during ischemia-reperfusion injury.","method":"Co-immunoprecipitation, ubiquitination assay, MG132 proteasome inhibition, in vivo SCIRI rat model, adenovirus overexpression","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination, in vivo model with rescue, single lab","pmids":["37591122"],"is_preprint":false},{"year":2023,"finding":"SYVN1 promotes ubiquitination and degradation of STAT3 in retinal microvascular endothelial cells; SYVN1 overexpression reduces phospho-STAT3, VEGF secretion, and neovascularization in an OIR mouse model, with effects rescued by STAT3 activator treatment.","method":"Co-immunoprecipitation, ubiquitination assay, intravitreal adenovirus injection, retinal flatmount analysis, electroretinogram","journal":"Investigative ophthalmology & visual science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination, in vivo mouse model with pharmacological rescue, single lab","pmids":["37540175"],"is_preprint":false},{"year":2020,"finding":"Exogenous H2S (NaHS) induces S-sulfhydration of Hrd1 at Cys115, enhancing Hrd1 interaction with VAMP3 and promoting VAMP3 ubiquitylation; Hrd1 C115A mutant abolishes VAMP3 ubiquitylation, CD36 membrane retention, and lipid droplet reduction in diabetic cardiomyocytes.","method":"S-sulfhydration assay, site-directed mutagenesis (C115A), Co-immunoprecipitation, LC-MS/MS ubiquitylation analysis, db/db mouse model","journal":"Aging and disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — PTM (S-sulfhydration) identified by biochemical assay with C115A mutagenesis, in vivo model, single lab","pmids":["32257542"],"is_preprint":false},{"year":2021,"finding":"H2S-induced S-sulfhydration of Hrd1 at Cys115 enhances Hrd1 interaction with DGAT1 and DGAT2, promoting their ubiquitylation and reducing lipid droplet accumulation in diabetic cardiac tissue; Hrd1 C115A mutation abolishes this interaction and effect.","method":"S-sulfhydration assay, site-directed mutagenesis (C115A), Co-immunoprecipitation, ubiquitylation assay, db/db mouse model","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — PTM with mutagenesis validation, Co-IP, ubiquitination, in vivo model, single lab","pmids":["34562065"],"is_preprint":false},{"year":2023,"finding":"Exogenous H2S promotes S-sulfhydration of Syvn1 at Cys115, facilitating Syvn1-Keap1 interaction and Keap1 ubiquitination, which activates Nrf2 nuclear translocation and the Nrf2/GPx4/GSH pathway to suppress ferroptosis in diabetic cardiomyocytes; Syvn1 C115A mutant partially attenuates these effects.","method":"S-sulfhydration assay, Syvn1 C115A mutagenesis, Co-immunoprecipitation, ubiquitination assay, db/db mouse model, Nrf2 nuclear translocation assay","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — PTM with site mutagenesis, Co-IP, in vivo model, single lab","pmids":["37875467"],"is_preprint":false},{"year":2022,"finding":"SYVN1 competitively interacts with TRIM59, preventing SYVN1-mediated TRIM59 ubiquitination and stabilizing TRIM59 expression; stable TRIM59 then promotes p53 degradation, thereby inhibiting ferroptosis in pancreatic cancer cells.","method":"Co-immunoprecipitation, ubiquitination assay, competitive binding assay, in vitro and in vivo tumor models","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, competitive interaction, in vivo PDX model, single lab","pmids":["37740007"],"is_preprint":false},{"year":2021,"finding":"SYVN1 interacts with ETS1 and promotes its ubiquitination at K318, leading to proteasomal degradation of ETS1 and downregulation of xCT/SLC7A11 transcription, thereby inducing ferroptosis in breast cancer cells; a small molecule (sculponeatin A) promotes the ETS1-SYVN1 interaction to enhance this effect.","method":"Co-immunoprecipitation, ubiquitination site mapping (K318), Western blot, ferroptosis assays, in vivo mouse tumor model","journal":"Phytomedicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination site mutagenesis, functional ferroptosis readout, in vivo model, single lab","pmids":["37327642"],"is_preprint":false},{"year":2015,"finding":"HRD1 transmembrane domain transfers Pael-R from the ER to the cytosol, while the proline-rich domain is required to promote Pael-R degradation; the transmembrane domain also stabilizes HRD1 itself.","method":"Domain deletion mutagenesis, Pael-R degradation assay, HRD1 stability analysis","journal":"Journal of pharmacological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mutagenesis with functional substrate transfer and stability readouts, single lab","pmids":["18344614"],"is_preprint":false},{"year":2022,"finding":"SEL1L-HRD1 ERAD degrades nascent WNT5A in a quality-control capacity; in the absence of ERAD, WNT5A misfolds and forms high-molecular-weight ER aggregates (loss of function), attenuating WNT5A-mediated suppression of hepatocyte proliferation and promoting tumorigenesis.","method":"Hepatocyte-specific Sel1L/Hrd1 knockout, proteomics substrate screen, WNT5A aggregation analysis, tumor mouse model","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — tissue-specific knockout, proteomics, WNT5A functional loss-of-function mechanism, single lab","pmids":["36238898"],"is_preprint":false},{"year":2023,"finding":"SEL1L-HRD1 ERAD degrades ceruloplasmin (CP), a key ferroxidase for systemic iron distribution; in the absence of ERAD, CP accumulates in the ER, is shunted to refolding, and is secreted at elevated levels, altering systemic iron homeostasis in a manner independent of ER stress.","method":"Hepatocyte-specific Sel1L knockout, proteomics substrate screen, CP secretion assay, iron homeostasis phenotyping in mice","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — tissue-specific knockout, proteomics, mechanistic substrate analysis, single lab","pmids":["36595688"],"is_preprint":false},{"year":2023,"finding":"SEL1L-HRD1 ERAD degrades the GPI-transamidase catalytic subunit PIGK, attenuating the biogenesis of GPI-anchored proteins; disease-causing PIGK variants in inherited GPI deficiency disorders are also SEL1L-HRD1 ERAD substrates.","method":"SILAC-based quantitative proteomics with machine learning filtering, ERAD substrate validation (PIGK), GPI-anchored protein functional assay, in vitro and in vivo models","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — proteomics with stringent filtering, functional validation in multiple cell types and in vivo, disease variant analysis","pmids":["38253565"],"is_preprint":false},{"year":2021,"finding":"SYVN1/HRD1 interacts with HSP90 and impacts ubiquitination of eukaryotic elongation factor 2 kinase (EEF2K) in hepatocellular carcinoma cells; SYVN1 knockdown inhibits HCC migration and invasion.","method":"Co-IP-based proteomics/mass spectrometry, immunofluorescence, Co-immunoprecipitation, ubiquitination assay","journal":"Cancer communications (London, England)","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS identification, limited mechanistic follow-up of the SYVN1-HSP90-EEF2K axis, single lab","pmids":["34196494"],"is_preprint":false},{"year":2013,"finding":"Hrd1 regulates collagen I maturation in renal fibrosis via the Sec23A-dependent ER-to-Golgi trafficking pathway; Hrd1 overexpression increases secreted and mature collagen I, while Hrd1 knockdown predominantly reduces mature collagen I; Sec23A knockdown blocks the Hrd1-mediated increase in collagen secretion.","method":"siRNA knockdown (Hrd1 and Sec23A), overexpression, collagen I secretion/maturation measurement, epistasis via double knockdown","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis (Sec23A-Hrd1 double knockdown), functional trafficking readout, single lab","pmids":["24114659"],"is_preprint":false},{"year":2023,"finding":"Xbp1-induced Hrd1 ubiquitinates Nrf2, leading to its degradation and reduced antioxidant response in renal tubular cells; the QSLVPDI motif on Nrf2 constitutes the active site for its interaction with Hrd1; downregulation of XBP1 reduces Hrd1 expression and enhances Nrf2/HO-1 function to protect against renal ischemia-reperfusion injury.","method":"Co-immunoprecipitation, ubiquitination assay, XBP1 heterozygous knockout mouse, Nrf2 interaction domain mapping","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping, ubiquitination assay, in vivo mouse model, single lab","pmids":["33654072"],"is_preprint":false},{"year":2017,"finding":"SYVN1, an ERAD E3 ubiquitin ligase, promotes intra-ER degradation of GABAAα1 in the dorsal striatum; SYVN1 knockdown increases GABAAα1 protein levels within the ER; this is associated with methamphetamine-induced conditioned place preference.","method":"siRNA knockdown in primary neurons and in vivo, proteasome inhibitor treatment (MG132), subcellular (intra/extra-ER) fractionation","journal":"Frontiers in molecular neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown, subcellular fractionation, proteasome inhibition, functional behavioral readout, single lab","pmids":["29051727"],"is_preprint":false},{"year":2016,"finding":"Aβ42 oligomers enhance XBP-1s, which transcriptionally upregulates HRD1; HRD1 then acts as an endogenous downregulator of BACE1, reducing BACE1 expression and activity to lower Aβ production.","method":"XBP-1s overexpression, HRD1 knockdown, BACE1 activity assay, Aβ42 oligomer treatment","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pathway dissection with overexpression and knockdown, functional BACE1 activity assay, single lab","pmids":["27853315"],"is_preprint":false},{"year":2021,"finding":"HRD1-mediated METTL14 degradation is blocked when competing unfolded/misfolded proteins accumulate during ER stress, establishing a mechanism by which protein load competes with HRD1 substrate selection to switch UPR toward adaptation.","method":"METTL14 ubiquitination competition assay, ER stress induction, liver-specific knockout","journal":"Molecular cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — competition-based mechanistic assay, in vivo knockout, single lab","pmids":["34847358"],"is_preprint":false}],"current_model":"SYVN1/HRD1 is an ER-resident multi-spanning E3 ubiquitin ligase that forms the core retrotranslocation channel of the SEL1L-HRD1 ERAD complex; its RING-H2 domain catalyzes ubiquitin transfer (working with E2 enzymes including Ubc7/UBE2J1), autoubiquitination of specific RING-domain lysines opens a ubiquitin-gated pore for luminal substrate retrotranslocation, and cycles of autoubiquitination/deubiquitination (regulated by Ubp1/USP19, Hrd3/SEL1L, and Usa1) control channel activity; the complex recruits substrates via luminal lectins OS-9/XTP3-B through the SEL1L adaptor, and coordinates with Derlin-2 and HERP proteins for membrane substrate movement; beyond canonical ERAD, HRD1 ubiquitinates a broad range of non-misfolded substrates including Nrf2, BLIMP1, p27kip1, Fas, pre-BCR, TGF-β receptor 1, STING, MafA, METTL14, GSDMD, tau, CREBH, and many metabolic enzymes, and its activity is post-translationally regulated by S-sulfhydration at Cys115 and UFMylation at Lys610."},"narrative":{"mechanistic_narrative":"SYVN1 (HRD1) is an ER-resident, multi-spanning E3 ubiquitin ligase that constitutes the catalytic core of the SEL1L-HRD1 ER-associated degradation (ERAD) machinery, coupling recognition of misfolded ER proteins to their ubiquitination and retrotranslocation into the cytosol for proteasomal destruction [PMID:11139575, PMID:20100910]. Its cytosolic RING-H2 finger binds the E2 conjugating enzymes Ubc7/UBE2J1 and is strictly required for ubiquitination of soluble and membrane misfolded substrates; the RING is also the regulatory hub of the channel [PMID:11139575, PMID:10218484, PMID:21245296]. Reconstitution and structural work establish that HRD1 forms a membrane dimer that, upon autoubiquitination of specific RING-domain lysines, disassembles into active monomers and opens an aqueous, laterally gated pore through which substrate loops are threaded; substrate binding enlarges the pore and deubiquitination closes it, making the autoubiquitination/deubiquitination cycle the gate of retrotranslocation [PMID:27321670, PMID:28682307, PMID:32094691, PMID:35970394]. In the assembled complex HRD1 partners with SEL1L (which it reciprocally stabilizes and which recruits UBE2J1, Derlin and the luminal lectins OS-9/XTP3-B that capture glycosylated substrates), together with Der1/Derlin-2 and HERP proteins that form a second half-channel and govern substrate movement [PMID:18264092, PMID:32327568, PMID:21454652, PMID:38365914, PMID:23867461, PMID:24366871]. Beyond clearance of misfolded clients, HRD1 ubiquitinates a broad spectrum of folded regulatory proteins to control diverse physiology: it degrades Nrf2, BLIMP1, p27kip1, Fas, the pre-BCR, TGF-β receptor 1, STING, the ER-tethered transcription factor CREBH, MafA, and METTL14, thereby tuning antioxidant responses, immune-cell development and signaling, β-cell identity, and hepatic metabolic gene programs [PMID:24636985, PMID:25366967, PMID:27417417, PMID:27573825, PMID:27568564, PMID:32182217, PMID:30389664, PMID:37142791, PMID:34847358, PMID:32086291]. HRD1 expression is induced by the UPR through the IRE1-XBP1 branch, and its ligase activity is itself set by post-translational modification, including S-sulfhydration at Cys115 and UFMylation at Lys610, and by deubiquitinases that stabilize it [PMID:17967421, PMID:27827840, PMID:37795761, PMID:32257542]. Disease-causing variants that weaken the SEL1L-HRD1 interaction impair ERAD, and inherited GPI-deficiency PIGK variants are themselves HRD1 substrates, linking this machinery to human Mendelian disease [PMID:38365914, PMID:38253565].","teleology":[{"year":1999,"claim":"Established that the RING-H2 motif of Der3/Hrd1p is indispensable for degrading both soluble and membrane misfolded ER proteins, defining HRD1 as a catalytic, not merely scaffolding, ERAD component.","evidence":"Site-directed RING mutagenesis (C399S), in vivo degradation and dominant-negative/genetic suppression assays in S. cerevisiae","pmids":["10218484"],"confidence":"High","gaps":["Did not define the E2 partner or biochemical mechanism","Did not establish substrate recognition route"]},{"year":2001,"claim":"Defined HRD1 as the E3 ligase of ERAD by mapping its six-TM topology with cytosolic RING and showing direct RING-dependent binding to E2 Ubc7p and in vitro ubiquitination.","evidence":"Topology mapping, in vitro ubiquitination, Ubc7p binding, RING-mutant analysis","pmids":["11139575"],"confidence":"High","gaps":["No structural model of the channel","Retrotranslocation mechanism unresolved"]},{"year":2008,"claim":"Showed how luminal substrates reach HRD1, identifying OS-9/XTP3-B lectins that bind substrate and dock onto SEL1L via their MRH domains.","evidence":"Reciprocal Co-IP, siRNA degradation assays, domain mutagenesis in mammalian cells","pmids":["18264092"],"confidence":"High","gaps":["How lectin-bound substrate is handed to HRD1 catalysis not shown","GRP94 role only correlative"]},{"year":2010,"claim":"Defined the architecture and codependence of the mammalian complex: HRD1 stabilizes SEL1L, and disposal of soluble ERAD-L substrates strictly requires HRD1, SEL1L and OS-9/XTP3-B.","evidence":"siRNA knockdown, reciprocal Co-IP, size fractionation, pulse-chase epistasis with defined substrates","pmids":["21454652","20100910"],"confidence":"High","gaps":["Distinct organization from yeast (Complex I vs II) not mechanistically explained","Stoichiometry undefined"]},{"year":2016,"claim":"Demonstrated that HRD1 autoubiquitination within its RING domain — not substrate ubiquitination or Cdc48 — triggers retrotranslocation of luminal domains, reordering the canonical ERAD sequence.","evidence":"Proteoliposome reconstitution with purified yeast proteins, RING-lysine mutagenesis, in vivo validation","pmids":["27321670"],"confidence":"High","gaps":["Did not visualize the channel","Did not resolve substrate paths through the membrane"]},{"year":2017,"claim":"Provided structural proof of a retrotranslocation channel, showing Hrd1 dimerizes with an eight-TM aqueous cavity and lateral gate in complex with Hrd3.","evidence":"Cryo-EM of S. cerevisiae Hrd1-Hrd3","pmids":["28682307"],"confidence":"High","gaps":["Captured an inactive state","Did not include Der1 half-channel or substrate"]},{"year":2020,"claim":"Unified structure and function: the five-subunit complex shows Hrd1 and Der1 form two opposing half-channels in a thinned membrane while Hrd3/Yos9 build a luminal substrate site, and purified Hrd1 forms a ubiquitination-gated pore enlarged by substrate.","evidence":"Cryo-EM of subcomplexes with crosslinking and MD; pore reconstitution with electrophysiology and RING-lysine mutagenesis","pmids":["32327568","32094691"],"confidence":"High","gaps":["Dynamics of dimer-to-monomer transition during catalysis not directly observed","Mammalian channel structure not solved"]},{"year":2022,"claim":"Mapped the substrate path in living cells and showed autoubiquitination disassembles inactive Hrd1 dimers into active monomers, linking the gating cycle to oligomeric state.","evidence":"Site-specific disulfide crosslinking in live yeast integrated with cryo-EM","pmids":["35970394"],"confidence":"High","gaps":["Kinetics of monomer activation not quantified","Generality across non-glycosylated substrates untested"]},{"year":2019,"claim":"Defined the writer/eraser logic of channel gating: deubiquitinase Ubp1 reverses autoubiquitination, Hrd3 brakes it, and Usa1 attenuates Ubp1, establishing a regulated cycle.","evidence":"Genetic and biochemical ubiquitination/deubiquitination assays with domain mutagenesis in S. cerevisiae","pmids":["31713515"],"confidence":"High","gaps":["Mammalian counterparts of this cycle not mapped here","Quantitative balance under stress unknown"]},{"year":2024,"claim":"Connected complex assembly to human disease, showing SEL1L-HRD1 binding recruits UBE2J1 and DERLIN and that a pathogenic SEL1L variant disrupts the interaction by electrostatic repulsion at the SEL1L/HRD1 interface.","evidence":"Interactome proteomics, interface mutagenesis, mouse model of pathogenic variant","pmids":["38365914"],"confidence":"High","gaps":["Full spectrum of affected substrates in patients not defined","Other interface mutations untested"]},{"year":2011,"claim":"Extended HRD1 ERAD to a physiological glycoprotein, showing HRD1/UBE2J1 dislocate misfolded MHC I heavy chains while sparing assembled heterotrimers, demonstrating substrate discrimination.","evidence":"siRNA screen, Co-IP complex characterization, ubiquitination and dislocation assays","pmids":["21245296"],"confidence":"High","gaps":["Molecular basis of discrimination unresolved","Role in antigen presentation only correlative"]},{"year":2014,"claim":"Revealed HRD1 as a regulator of folded transcription factors beyond ERAD, degrading Nrf2 (independently of Keap1) and BLIMP1 to control antioxidant responses and dendritic-cell MHC-II expression.","evidence":"Conditional knockout mice, ubiquitination assays, human tissue analysis, T-cell priming assays","pmids":["24636985","25366967"],"confidence":"High","gaps":["How HRD1 recognizes cytosolic/non-ER substrates unclear","Linkage to canonical ERAD machinery not established for these substrates"]},{"year":2016,"claim":"Established HRD1 control of immune-cell fate by degrading p27kip1, Fas, and the pre-BCR, with genetic epistasis defining causal substrates for proliferation, survival, and developmental checkpoints.","evidence":"Conditional Hrd1/Sel1L knockouts with p27 and Fas rescue crosses, ubiquitination and signaling assays","pmids":["27417417","27573825","27568564"],"confidence":"High","gaps":["Substrate selectivity mechanisms across these clients not defined","Localization of these degradation events not resolved"]},{"year":2020,"claim":"Demonstrated HRD1/SEL1L control of cell identity and innate immunity, degrading TGF-β receptor 1 (β-cell identity), MafA (insulin secretion), and STING (basal antiviral tone).","evidence":"Tissue-specific knockouts/overexpression, scRNA-seq, ubiquitination assays, viral/tumor and pharmacological rescue models","pmids":["32182217","32086291","37142791"],"confidence":"High","gaps":["Whether these substrates use the retrotranslocation channel or a distinct route is unresolved","Quantitative contribution relative to other ligases unknown"]},{"year":2018,"claim":"Defined a hepatic ERAD-CREBH-FGF21 metabolic axis and a broader metabolic-enzyme degradome (ENTPD5, CPT2, RMND1, HSD17B4), showing HRD1 ubiquitination of CREBH at K294 sets postprandial FGF21 and reprograms hepatic metabolism.","evidence":"Liver-specific knockouts, ubiquitination site mapping, refeeding studies, interactome proteomics, metabolic phenotyping","pmids":["30389665","30389664","30201971"],"confidence":"High","gaps":["Direct vs indirect effects on some metabolic enzymes not fully separated","Tissue specificity of substrate set unexplained"]},{"year":2021,"claim":"Linked HRD1 substrate selection to UPR outcome, showing accumulating misfolded proteins competitively block METTL14 degradation, raising m6A modification of CHOP mRNA to bias cells toward adaptation.","evidence":"Ubiquitination competition assays, m6A analysis, liver-specific knockouts","pmids":["34847358"],"confidence":"High","gaps":["Generality of competitive substrate triage to other clients untested","Affinity hierarchy of substrates undefined"]},{"year":2023,"claim":"Identified post-translational control of HRD1 activity via UFMylation at Lys610 and discovered new quality-control substrates (PIGK in GPI biogenesis, ceruloplasmin), including disease-relevant variants.","evidence":"UFMylation and ubiquitination assays with K610R mutagenesis; SILAC proteomics with functional and in vivo substrate validation","pmids":["37795761","38253565"],"confidence":"High","gaps":["Interplay between UFMylation, S-sulfhydration, and autoubiquitination not integrated","Full substrate repertoire still expanding"]},{"year":null,"claim":"How HRD1 selects and engages its many non-canonical, folded cytosolic substrates relative to the structurally defined luminal retrotranslocation pathway remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model for cytosolic substrate engagement","Mechanism integrating PTM regulation with substrate triage unknown","Tissue-specific substrate repertoire incompletely mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1,3,12]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,13,20,21,38]},{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[3,6]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[4,5,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[36,44]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,4,9,31]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,3,10,11]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[33,38,71]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[12,14,17,21,36]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[18,20,45,53]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[3,6,26]}],"complexes":["SEL1L-HRD1 ERAD complex","HRD1-Hrd3-Der1-Usa1-Yos9 retrotranslocon","ERpQC (HRD1-Sec61α-Derlin-1) complex"],"partners":["SEL1L","UBE2J1","OS-9","DERL2","HERP","HRD3","YOS9","USP15"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86TM6","full_name":"E3 ubiquitin-protein ligase synoviolin","aliases":["RING-type E3 ubiquitin transferase synoviolin","Synovial apoptosis inhibitor 1"],"length_aa":617,"mass_kda":67.7,"function":"E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:27827840, PubMed:26471130, PubMed:28827405). Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130, PubMed:28842558). Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Protects neurons from apoptosis induced by polyglutamine-expanded huntingtin (HTT) or unfolded GPR37 by promoting their degradation (PubMed:17141218). Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis (PubMed:17170702). Mediates the ubiquitination and subsequent degradation of cytoplasmic NFE2L1 (By similarity). During the early stage of B cell development, required for degradation of the pre-B cell receptor (pre-BCR) complex, hence supporting further differentiation into mature B cells (By similarity)","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q86TM6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SYVN1","classification":"Common Essential","n_dependent_lines":474,"n_total_lines":1208,"dependency_fraction":0.3923841059602649},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000162298","cell_line_id":"CID000363","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"GATAD2A","stoichiometry":0.2},{"gene":"OS9","stoichiometry":0.2},{"gene":"SEL1L","stoichiometry":0.2},{"gene":"HSPA5","stoichiometry":0.2},{"gene":"HSPA4","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000363","total_profiled":1310},"omim":[{"mim_id":"620640","title":"RING FINGER PROTEIN 145; RNF145","url":"https://www.omim.org/entry/620640"},{"mim_id":"616215","title":"cAMP RESPONSE ELEMENT-BINDING PROTEIN 3-LIKE 1; CREB3L1","url":"https://www.omim.org/entry/616215"},{"mim_id":"616175","title":"UBIQUITIN-CONJUGATING ENZYME E2 J1; UBE2J1","url":"https://www.omim.org/entry/616175"},{"mim_id":"613777","title":"FAD-DEPENDENT OXIDOREDUCTASE DOMAIN-CONTAINING PROTEIN 2; FOXRED2","url":"https://www.omim.org/entry/613777"},{"mim_id":"610304","title":"DER1-LIKE DOMAIN FAMILY, MEMBER 2; DERL2","url":"https://www.omim.org/entry/610304"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Endoplasmic reticulum","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SYVN1"},"hgnc":{"alias_symbol":["HRD1","DER3"],"prev_symbol":[]},"alphafold":{"accession":"Q86TM6","domains":[{"cath_id":"3.30.40.10","chopping":"270-337","consensus_level":"medium","plddt":85.4743,"start":270,"end":337},{"cath_id":"1.10.287","chopping":"2-67","consensus_level":"medium","plddt":92.1824,"start":2,"end":67},{"cath_id":"1.20.190","chopping":"70-264","consensus_level":"high","plddt":92.1983,"start":70,"end":264}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86TM6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86TM6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86TM6-F1-predicted_aligned_error_v6.png","plddt_mean":72.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SYVN1","jax_strain_url":"https://www.jax.org/strain/search?query=SYVN1"},"sequence":{"accession":"Q86TM6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86TM6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86TM6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86TM6"}},"corpus_meta":[{"pmid":"18264092","id":"PMC_18264092","title":"OS-9 and GRP94 deliver mutant alpha1-antitrypsin to the Hrd1-SEL1L ubiquitin ligase complex for ERAD.","date":"2008","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/18264092","citation_count":420,"is_preprint":false},{"pmid":"24636985","id":"PMC_24636985","title":"Hrd1 suppresses Nrf2-mediated cellular protection during liver cirrhosis.","date":"2014","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/24636985","citation_count":313,"is_preprint":false},{"pmid":"32327568","id":"PMC_32327568","title":"Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.","date":"2020","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/32327568","citation_count":196,"is_preprint":false},{"pmid":"12975321","id":"PMC_12975321","title":"Synoviolin/Hrd1, an E3 ubiquitin ligase, as a novel pathogenic factor for arthropathy.","date":"2003","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/12975321","citation_count":168,"is_preprint":false},{"pmid":"27321670","id":"PMC_27321670","title":"Autoubiquitination of the Hrd1 Ligase Triggers Protein Retrotranslocation in ERAD.","date":"2016","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/27321670","citation_count":164,"is_preprint":false},{"pmid":"20237263","id":"PMC_20237263","title":"Loss of HRD1-mediated protein degradation causes amyloid precursor protein accumulation and amyloid-beta generation.","date":"2010","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/20237263","citation_count":162,"is_preprint":false},{"pmid":"28682307","id":"PMC_28682307","title":"Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28682307","citation_count":160,"is_preprint":false},{"pmid":"20100910","id":"PMC_20100910","title":"Stringent requirement for HRD1, SEL1L, and OS-9/XTP3-B for disposal of ERAD-LS substrates.","date":"2010","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20100910","citation_count":148,"is_preprint":false},{"pmid":"11139575","id":"PMC_11139575","title":"Membrane topology and function of Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endoplasmic reticulum degradation.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11139575","citation_count":144,"is_preprint":false},{"pmid":"21245296","id":"PMC_21245296","title":"HRD1 and UBE2J1 target misfolded MHC class I heavy chains for endoplasmic reticulum-associated degradation.","date":"2011","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/21245296","citation_count":120,"is_preprint":false},{"pmid":"32066502","id":"PMC_32066502","title":"LncRNA SNHG7/miR-34a-5p/SYVN1 axis plays a vital role in proliferation, apoptosis and autophagy in osteoarthritis.","date":"2020","source":"Biological research","url":"https://pubmed.ncbi.nlm.nih.gov/32066502","citation_count":117,"is_preprint":false},{"pmid":"26137860","id":"PMC_26137860","title":"Hrd1 and ER-Associated Protein Degradation, ERAD, are Critical Elements of the Adaptive ER Stress Response in Cardiac Myocytes.","date":"2015","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/26137860","citation_count":113,"is_preprint":false},{"pmid":"33530981","id":"PMC_33530981","title":"CircNR3C2 promotes HRD1-mediated tumor-suppressive effect via sponging miR-513a-3p in triple-negative breast cancer.","date":"2021","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/33530981","citation_count":104,"is_preprint":false},{"pmid":"23710284","id":"PMC_23710284","title":"Endoplasmic reticulum stress and Parkinson's disease: the role of HRD1 in averting apoptosis in neurodegenerative disease.","date":"2013","source":"Oxidative medicine and cellular longevity","url":"https://pubmed.ncbi.nlm.nih.gov/23710284","citation_count":103,"is_preprint":false},{"pmid":"37224754","id":"PMC_37224754","title":"Endoplasmic reticulum stress-triggered ferroptosis via the XBP1-Hrd1-Nrf2 pathway induces EMT progression in diabetic nephropathy.","date":"2023","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/37224754","citation_count":102,"is_preprint":false},{"pmid":"21454652","id":"PMC_21454652","title":"SEL1L protein critically determines the stability of the HRD1-SEL1L endoplasmic reticulum-associated degradation (ERAD) complex to optimize the degradation kinetics of ERAD substrates.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21454652","citation_count":95,"is_preprint":false},{"pmid":"17141218","id":"PMC_17141218","title":"Ubiquitin ligase Hrd1 enhances the degradation and suppresses the toxicity of polyglutamine-expanded huntingtin.","date":"2006","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/17141218","citation_count":92,"is_preprint":false},{"pmid":"25366967","id":"PMC_25366967","title":"Hrd1-mediated BLIMP-1 ubiquitination promotes dendritic cell MHCII expression for CD4 T cell priming during inflammation.","date":"2014","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/25366967","citation_count":86,"is_preprint":false},{"pmid":"37142791","id":"PMC_37142791","title":"SEL1L-HRD1 endoplasmic reticulum-associated degradation controls STING-mediated innate immunity by limiting the size of the activable STING pool.","date":"2023","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/37142791","citation_count":84,"is_preprint":false},{"pmid":"32182217","id":"PMC_32182217","title":"Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-β signaling.","date":"2020","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/32182217","citation_count":80,"is_preprint":false},{"pmid":"30389665","id":"PMC_30389665","title":"Hepatic Sel1L-Hrd1 ER-associated degradation (ERAD) manages FGF21 levels and systemic metabolism via CREBH.","date":"2018","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/30389665","citation_count":80,"is_preprint":false},{"pmid":"17059562","id":"PMC_17059562","title":"A ubiquitin ligase HRD1 promotes the degradation of Pael receptor, a substrate of Parkin.","date":"2006","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17059562","citation_count":78,"is_preprint":false},{"pmid":"17967421","id":"PMC_17967421","title":"A different pathway in the endoplasmic reticulum stress-induced expression of human HRD1 and SEL1 genes.","date":"2007","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/17967421","citation_count":72,"is_preprint":false},{"pmid":"32094691","id":"PMC_32094691","title":"Hrd1 forms the retrotranslocation pore regulated by auto-ubiquitination and binding of misfolded proteins.","date":"2020","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/32094691","citation_count":67,"is_preprint":false},{"pmid":"27568564","id":"PMC_27568564","title":"The Sel1L-Hrd1 Endoplasmic Reticulum-Associated Degradation Complex Manages a Key Checkpoint in B Cell Development.","date":"2016","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27568564","citation_count":67,"is_preprint":false},{"pmid":"34847358","id":"PMC_34847358","title":"HRD1-mediated METTL14 degradation regulates m6A mRNA modification to suppress ER proteotoxic liver disease.","date":"2021","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/34847358","citation_count":66,"is_preprint":false},{"pmid":"24478453","id":"PMC_24478453","title":"Herp coordinates compartmentalization and recruitment of HRD1 and misfolded proteins for ERAD.","date":"2014","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/24478453","citation_count":65,"is_preprint":false},{"pmid":"30201971","id":"PMC_30201971","title":"ER-associated ubiquitin ligase HRD1 programs liver metabolism by targeting multiple metabolic enzymes.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30201971","citation_count":63,"is_preprint":false},{"pmid":"19864457","id":"PMC_19864457","title":"The E3 ubiquitin ligases Hrd1 and gp78 bind to and promote cholera toxin retro-translocation.","date":"2009","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/19864457","citation_count":63,"is_preprint":false},{"pmid":"21149444","id":"PMC_21149444","title":"Herp regulates Hrd1-mediated ubiquitylation in a ubiquitin-like domain-dependent manner.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21149444","citation_count":60,"is_preprint":false},{"pmid":"30389664","id":"PMC_30389664","title":"HRD1-ERAD controls production of the hepatokine FGF21 through CREBH polyubiquitination.","date":"2018","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/30389664","citation_count":59,"is_preprint":false},{"pmid":"31490085","id":"PMC_31490085","title":"Octyl itaconate inhibits osteoclastogenesis by suppressing Hrd1 and activating Nrf2 signaling.","date":"2019","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/31490085","citation_count":57,"is_preprint":false},{"pmid":"32888949","id":"PMC_32888949","title":"Hrd1-mediated ACLY ubiquitination alleviate NAFLD in db/db mice.","date":"2020","source":"Metabolism: clinical and experimental","url":"https://pubmed.ncbi.nlm.nih.gov/32888949","citation_count":56,"is_preprint":false},{"pmid":"19828134","id":"PMC_19828134","title":"Differential regulation of CFTRDeltaF508 degradation by ubiquitin ligases gp78 and Hrd1.","date":"2009","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/19828134","citation_count":56,"is_preprint":false},{"pmid":"27417417","id":"PMC_27417417","title":"The ER membrane-anchored ubiquitin ligase Hrd1 is a positive regulator of T-cell immunity.","date":"2016","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/27417417","citation_count":55,"is_preprint":false},{"pmid":"37875467","id":"PMC_37875467","title":"Exogenous H2S initiating Nrf2/GPx4/GSH pathway through promoting Syvn1-Keap1 interaction in diabetic hearts.","date":"2023","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/37875467","citation_count":53,"is_preprint":false},{"pmid":"28121484","id":"PMC_28121484","title":"Ubiquitin ligase SYVN1/HRD1 facilitates degradation of the SERPINA1 Z variant/α-1-antitrypsin Z variant via SQSTM1/p62-dependent selective autophagy.","date":"2017","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/28121484","citation_count":53,"is_preprint":false},{"pmid":"30843874","id":"PMC_30843874","title":"The E3 ligase Hrd1 stabilizes Tregs by antagonizing inflammatory cytokine-induced ER stress response.","date":"2019","source":"JCI insight","url":"https://pubmed.ncbi.nlm.nih.gov/30843874","citation_count":53,"is_preprint":false},{"pmid":"35115505","id":"PMC_35115505","title":"E3 ubiquitin ligase SYVN1 is a key positive regulator for GSDMD-mediated pyroptosis.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35115505","citation_count":52,"is_preprint":false},{"pmid":"33654072","id":"PMC_33654072","title":"Downregulation of XBP1 protects kidney against ischemia-reperfusion injury via suppressing HRD1-mediated NRF2 ubiquitylation.","date":"2021","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/33654072","citation_count":52,"is_preprint":false},{"pmid":"32086291","id":"PMC_32086291","title":"HRD1, an Important Player in Pancreatic β-Cell Failure and Therapeutic Target for Type 2 Diabetic Mice.","date":"2020","source":"Diabetes","url":"https://pubmed.ncbi.nlm.nih.gov/32086291","citation_count":51,"is_preprint":false},{"pmid":"29233968","id":"PMC_29233968","title":"HRD1 prevents apoptosis in renal tubular epithelial cells by mediating eIF2α ubiquitylation and degradation.","date":"2017","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/29233968","citation_count":50,"is_preprint":false},{"pmid":"31932479","id":"PMC_31932479","title":"E3 Ubiquitin Ligase HRD1 Promotes Lung Tumorigenesis by Promoting Sirtuin 2 Ubiquitination and Degradation.","date":"2020","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31932479","citation_count":49,"is_preprint":false},{"pmid":"31477895","id":"PMC_31477895","title":"ER-localized Hrd1 ubiquitinates and inactivates Usp15 to promote TLR4-induced inflammation during bacterial infection.","date":"2019","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31477895","citation_count":48,"is_preprint":false},{"pmid":"32057541","id":"PMC_32057541","title":"Endoplasmic reticulum-associated degradation and beyond: The multitasking roles for HRD1 in immune regulation and autoimmunity.","date":"2020","source":"Journal of autoimmunity","url":"https://pubmed.ncbi.nlm.nih.gov/32057541","citation_count":47,"is_preprint":false},{"pmid":"23867461","id":"PMC_23867461","title":"Derlin2 protein facilitates HRD1-mediated retro-translocation of sonic hedgehog at the endoplasmic reticulum.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23867461","citation_count":46,"is_preprint":false},{"pmid":"10218484","id":"PMC_10218484","title":"A RING-H2 finger motif is essential for the function of Der3/Hrd1 in endoplasmic reticulum associated protein degradation in the yeast Saccharomyces cerevisiae.","date":"1999","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/10218484","citation_count":44,"is_preprint":false},{"pmid":"31713515","id":"PMC_31713515","title":"Cycles of autoubiquitination and deubiquitination regulate the ERAD ubiquitin ligase Hrd1.","date":"2019","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/31713515","citation_count":44,"is_preprint":false},{"pmid":"34196494","id":"PMC_34196494","title":"Integrative proteomics reveals the role of E3 ubiquitin ligase SYVN1 in hepatocellular carcinoma metastasis.","date":"2021","source":"Cancer communications (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/34196494","citation_count":43,"is_preprint":false},{"pmid":"24366871","id":"PMC_24366871","title":"Role of HERP and a HERP-related protein in HRD1-dependent protein degradation at the endoplasmic reticulum.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24366871","citation_count":43,"is_preprint":false},{"pmid":"33207079","id":"PMC_33207079","title":"HRD1 inhibits fatty acid oxidation and tumorigenesis by ubiquitinating CPT2 in triple-negative breast cancer.","date":"2020","source":"Molecular oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33207079","citation_count":41,"is_preprint":false},{"pmid":"18314878","id":"PMC_18314878","title":"SEL1L and HRD1 are involved in the degradation of unassembled secretory Ig-mu chains.","date":"2008","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/18314878","citation_count":39,"is_preprint":false},{"pmid":"27573825","id":"PMC_27573825","title":"Endoplasmic reticulum-resident E3 ubiquitin ligase Hrd1 controls B-cell immunity through degradation of the death receptor CD95/Fas.","date":"2016","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/27573825","citation_count":39,"is_preprint":false},{"pmid":"26945068","id":"PMC_26945068","title":"Grp94 Protein Delivers γ-Aminobutyric Acid Type A (GABAA) Receptors to Hrd1 Protein-mediated Endoplasmic Reticulum-associated Degradation.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26945068","citation_count":39,"is_preprint":false},{"pmid":"29743537","id":"PMC_29743537","title":"Molecular mechanism of ER stress-induced pre-emptive quality control involving association of the translocon, Derlin-1, and HRD1.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29743537","citation_count":38,"is_preprint":false},{"pmid":"29958993","id":"PMC_29958993","title":"HRD1-mediated PTEN degradation promotes cell proliferation and hepatocellular carcinoma progression.","date":"2018","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/29958993","citation_count":37,"is_preprint":false},{"pmid":"26536657","id":"PMC_26536657","title":"HRD1 suppresses the growth and metastasis of breast cancer cells by promoting IGF-1R degradation.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26536657","citation_count":37,"is_preprint":false},{"pmid":"28411238","id":"PMC_28411238","title":"Characterization of protein complexes of the endoplasmic reticulum-associated degradation E3 ubiquitin ligase Hrd1.","date":"2017","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28411238","citation_count":37,"is_preprint":false},{"pmid":"18344614","id":"PMC_18344614","title":"Novel functions of ubiquitin ligase HRD1 with transmembrane and proline-rich domains.","date":"2008","source":"Journal of pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/18344614","citation_count":35,"is_preprint":false},{"pmid":"38365914","id":"PMC_38365914","title":"SEL1L-HRD1 interaction is required to form a functional HRD1 ERAD complex.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38365914","citation_count":34,"is_preprint":false},{"pmid":"30106139","id":"PMC_30106139","title":"Long non-coding RNA CASC2 inhibits breast cancer cell growth and metastasis through the regulation of the miR-96-5p/SYVN1 pathway.","date":"2018","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/30106139","citation_count":34,"is_preprint":false},{"pmid":"18241051","id":"PMC_18241051","title":"Immunohistochemical localization of a ubiquitin ligase HRD1 in murine brain.","date":"2008","source":"Journal of neuroscience research","url":"https://pubmed.ncbi.nlm.nih.gov/18241051","citation_count":34,"is_preprint":false},{"pmid":"33588886","id":"PMC_33588886","title":"Anti-Warburg effect by targeting HRD1-PFKP pathway may inhibit breast cancer progression.","date":"2021","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/33588886","citation_count":33,"is_preprint":false},{"pmid":"28334804","id":"PMC_28334804","title":"A critical role of Hrd1 in the regulation of optineurin degradation and aggresome formation.","date":"2017","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28334804","citation_count":33,"is_preprint":false},{"pmid":"37591122","id":"PMC_37591122","title":"SYVN1 attenuates ferroptosis and alleviates spinal cord ischemia-reperfusion injury in rats by regulating the HMGB1/NRF2/HO-1 axis.","date":"2023","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/37591122","citation_count":32,"is_preprint":false},{"pmid":"37943610","id":"PMC_37943610","title":"Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are associated with neurodevelopmental disorders.","date":"2024","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/37943610","citation_count":32,"is_preprint":false},{"pmid":"32257542","id":"PMC_32257542","title":"Exogenous H2S Induces Hrd1 S-sulfhydration and Prevents CD36 Translocation via VAMP3 Ubiquitylation in Diabetic Hearts.","date":"2020","source":"Aging and disease","url":"https://pubmed.ncbi.nlm.nih.gov/32257542","citation_count":32,"is_preprint":false},{"pmid":"34562065","id":"PMC_34562065","title":"Hydrogen sulphide reduced the accumulation of lipid droplets in cardiac tissues of db/db mice via Hrd1 S-sulfhydration.","date":"2021","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34562065","citation_count":30,"is_preprint":false},{"pmid":"27756846","id":"PMC_27756846","title":"SYVN1, NEDD8, and FBXO2 Proteins Regulate ΔF508 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Ubiquitin-mediated Proteasomal Degradation.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/27756846","citation_count":29,"is_preprint":false},{"pmid":"35279748","id":"PMC_35279748","title":"S100A16 promotes acute kidney injury by activating HRD1-induced ubiquitination and degradation of GSK3β and CK1α.","date":"2022","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/35279748","citation_count":28,"is_preprint":false},{"pmid":"37392829","id":"PMC_37392829","title":"Down-regulation of Hrd1 protects against myocardial ischemia-reperfusion injury by regulating PPARα to prevent oxidative stress, endoplasmic reticulum stress, and cellular apoptosis.","date":"2023","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/37392829","citation_count":28,"is_preprint":false},{"pmid":"32308114","id":"PMC_32308114","title":"HRD1 prevents atherosclerosis-mediated endothelial cell apoptosis by promoting LOX-1 degradation.","date":"2020","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/32308114","citation_count":27,"is_preprint":false},{"pmid":"27082896","id":"PMC_27082896","title":"HRD1-Mediated IGF-1R Ubiquitination Contributes to Renal Protection of Resveratrol in db/db Mice.","date":"2016","source":"Molecular endocrinology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/27082896","citation_count":27,"is_preprint":false},{"pmid":"27827840","id":"PMC_27827840","title":"USP19-Mediated Deubiquitination Facilitates the Stabilization of HRD1 Ubiquitin Ligase.","date":"2016","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/27827840","citation_count":26,"is_preprint":false},{"pmid":"33592335","id":"PMC_33592335","title":"Regulation of hepatic circadian metabolism by the E3 ubiquitin ligase HRD1-controlled CREBH/PPARα transcriptional program.","date":"2021","source":"Molecular metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/33592335","citation_count":25,"is_preprint":false},{"pmid":"24114659","id":"PMC_24114659","title":"Hrd1 participates in the regulation of collagen I synthesis in renal fibrosis.","date":"2013","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24114659","citation_count":25,"is_preprint":false},{"pmid":"36238898","id":"PMC_36238898","title":"SEL1L-HRD1 ER-associated degradation suppresses hepatocyte hyperproliferation and liver cancer.","date":"2022","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/36238898","citation_count":24,"is_preprint":false},{"pmid":"37740007","id":"PMC_37740007","title":"SLC35F2-SYVN1-TRIM59 axis critically regulates ferroptosis of pancreatic cancer cells by inhibiting endogenous p53.","date":"2023","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/37740007","citation_count":23,"is_preprint":false},{"pmid":"38253565","id":"PMC_38253565","title":"Proteomic screens of SEL1L-HRD1 ER-associated degradation substrates reveal its role in glycosylphosphatidylinositol-anchored protein biogenesis.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38253565","citation_count":23,"is_preprint":false},{"pmid":"30306455","id":"PMC_30306455","title":"Upregulation of HRD1 promotes cell migration and invasion in colon cancer.","date":"2018","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30306455","citation_count":23,"is_preprint":false},{"pmid":"37327642","id":"PMC_37327642","title":"Sculponeatin A promotes the ETS1-SYVN1 interaction to induce SLC7A11/xCT-dependent ferroptosis in breast cancer.","date":"2023","source":"Phytomedicine : international journal of phytotherapy and phytopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/37327642","citation_count":23,"is_preprint":false},{"pmid":"30167107","id":"PMC_30167107","title":"Proteomic characterization of endogenous substrates of mammalian ubiquitin ligase Hrd1.","date":"2018","source":"Cell & bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/30167107","citation_count":23,"is_preprint":false},{"pmid":"20606367","id":"PMC_20606367","title":"Correlation between decrease in protein levels of ubiquitin ligase HRD1 and amyloid-beta production.","date":"2010","source":"Journal of pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/20606367","citation_count":23,"is_preprint":false},{"pmid":"22382662","id":"PMC_22382662","title":"Molecular approaches to the treatment, prophylaxis, and diagnosis of Alzheimer's disease: possible involvement of HRD1, a novel molecule related to endoplasmic reticulum stress, in Alzheimer's disease.","date":"2012","source":"Journal of pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/22382662","citation_count":23,"is_preprint":false},{"pmid":"36595688","id":"PMC_36595688","title":"Hepatic SEL1L-HRD1 ER-associated degradation regulates systemic iron homeostasis via ceruloplasmin.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/36595688","citation_count":22,"is_preprint":false},{"pmid":"22280354","id":"PMC_22280354","title":"Hrd1 facilitates tau degradation and promotes neuron survival.","date":"2012","source":"Current molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/22280354","citation_count":22,"is_preprint":false},{"pmid":"30475171","id":"PMC_30475171","title":"Both thapsigargin- and tunicamycin-induced endoplasmic reticulum stress increases expression of Hrd1 in IRE1-dependent fashion.","date":"2018","source":"Neurological research","url":"https://pubmed.ncbi.nlm.nih.gov/30475171","citation_count":22,"is_preprint":false},{"pmid":"37795761","id":"PMC_37795761","title":"UFMylation of HRD1 regulates endoplasmic reticulum homeostasis.","date":"2023","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/37795761","citation_count":21,"is_preprint":false},{"pmid":"26358086","id":"PMC_26358086","title":"Experimental study of the protective effects of SYVN1 against diabetic retinopathy.","date":"2015","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26358086","citation_count":20,"is_preprint":false},{"pmid":"26471130","id":"PMC_26471130","title":"Association of the SEL1L protein transmembrane domain with HRD1 ubiquitin ligase regulates ERAD-L.","date":"2015","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/26471130","citation_count":20,"is_preprint":false},{"pmid":"27853315","id":"PMC_27853315","title":"Aβ42 oligomers modulate β-secretase through an XBP-1s-dependent pathway involving HRD1.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27853315","citation_count":20,"is_preprint":false},{"pmid":"35533759","id":"PMC_35533759","title":"HRD1 in human malignant neoplasms: Molecular mechanisms and novel therapeutic strategy for cancer.","date":"2022","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35533759","citation_count":19,"is_preprint":false},{"pmid":"29083378","id":"PMC_29083378","title":"Neuroprotection by Endoplasmic Reticulum Stress-Induced HRD1 and Chaperones: Possible Therapeutic Targets for Alzheimer's and Parkinson's Disease.","date":"2016","source":"Medical sciences (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/29083378","citation_count":19,"is_preprint":false},{"pmid":"36809917","id":"PMC_36809917","title":"HRD1 functions as a tumor suppressor in ovarian cancer by facilitating ubiquitination-dependent SLC7A11 degradation.","date":"2023","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/36809917","citation_count":19,"is_preprint":false},{"pmid":"35970394","id":"PMC_35970394","title":"Disulfide-crosslink analysis of the ubiquitin ligase Hrd1 complex during endoplasmic reticulum-associated protein degradation.","date":"2022","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35970394","citation_count":19,"is_preprint":false},{"pmid":"29051727","id":"PMC_29051727","title":"SYVN1, an ERAD E3 Ubiquitin Ligase, Is Involved in GABAAα1 Degradation Associated with Methamphetamine-Induced Conditioned Place Preference.","date":"2017","source":"Frontiers in molecular neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/29051727","citation_count":19,"is_preprint":false},{"pmid":"34820329","id":"PMC_34820329","title":"Epigenetic Regulator KDM4D Restricts Tumorigenesis via Modulating SYVN1/HMGB1 Ubiquitination Axis in Esophageal Squamous Cell Carcinoma.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34820329","citation_count":19,"is_preprint":false},{"pmid":"40562846","id":"PMC_40562846","title":"SEL1L-HRD1-mediated ERAD in mammals.","date":"2025","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/40562846","citation_count":18,"is_preprint":false},{"pmid":"37540175","id":"PMC_37540175","title":"SYVN1 Promotes STAT3 Protein Ubiquitination and Exerts Antiangiogenesis Effects in Retinopathy of Prematurity Development.","date":"2023","source":"Investigative ophthalmology & visual science","url":"https://pubmed.ncbi.nlm.nih.gov/37540175","citation_count":18,"is_preprint":false},{"pmid":"28423597","id":"PMC_28423597","title":"HRD1 sensitizes breast cancer cells to Tamoxifen by promoting S100A8 degradation.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/28423597","citation_count":18,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":51196,"output_tokens":16948,"usd":0.203904,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":30139,"output_tokens":5705,"usd":0.14666,"stage2_stop_reason":"end_turn"},"total_usd":0.350564,"stage1_batch_id":"msgbatch_015cW3C55o5xm8EPaM1UvcZR","stage2_batch_id":"msgbatch_018NDJHPntdYJzBohpB6hHKo","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"Der3/Hrd1p (SYVN1) is a six-transmembrane ER membrane protein with cytoplasmic N- and C-termini; its RING-H2 finger domain is required for ubiquitination of misfolded ER proteins, and it directly binds the E2 ubiquitin-conjugating enzyme Ubc7p through this RING domain, establishing it as the E3 ubiquitin ligase of the ERAD pathway.\",\n      \"method\": \"Membrane topology mapping, in vitro ubiquitination assay, Ubc7p binding assay, in vivo RING-finger mutant analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted in vitro ubiquitination, topology mapping, and mutational analysis in a single rigorous study\",\n      \"pmids\": [\"11139575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"The RING-H2 finger motif of Der3/Hrd1p is essential for ERAD function; a C399S point mutation abolishes degradation of both soluble and integral membrane misfolded ER proteins and acts as a dominant negative, while Hrd3p overexpression suppresses this dominant effect, suggesting competition for Hrd3p interaction.\",\n      \"method\": \"Site-directed mutagenesis, in vivo degradation assay, dominant-allele analysis, genetic suppression\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — mutagenesis plus genetic epistasis with multiple orthogonal readouts\",\n      \"pmids\": [\"10218484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"OS-9 and XTP3-B (Erlectin) are ER-resident glycoproteins that bind ERAD substrates (mutant α1-antitrypsin) and, through the SEL1L adaptor, deliver them to the HRD1 ubiquitin ligase complex; OS-9 also associates with the ER chaperone GRP94. The MRH domains of OS-9/XTP3-B are required for SEL1L interaction but not for substrate binding.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown with degradation assay, domain mutagenesis\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, domain mutagenesis, functional knockdown, replicated across two lectin paralogs\",\n      \"pmids\": [\"18264092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Autoubiquitination of Hrd1 within its RING-finger domain triggers retrotranslocation of misfolded luminal protein domains across the ER membrane in a reconstituted proteoliposome system; substrate ubiquitination is a subsequent event and the Cdc48 ATPase is not required for the retrotranslocation step itself.\",\n      \"method\": \"In vitro reconstitution with purified S. cerevisiae proteins in proteoliposomes, RING-finger lysine mutagenesis, in vivo ERAD assay\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — full biochemical reconstitution with purified components plus mutagenesis and in vivo validation\",\n      \"pmids\": [\"27321670\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Cryo-EM structure of S. cerevisiae Hrd1 in complex with Hrd3 shows Hrd1 forms a dimer in the membrane; each Hrd1 molecule has eight transmembrane segments with an aqueous cavity extending from the cytosol nearly to the ER lumen and a lateral gate, consistent with a retrotranslocation channel.\",\n      \"method\": \"Cryo-electron microscopy structural determination\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure with near-atomic resolution providing direct mechanistic insight\",\n      \"pmids\": [\"28682307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Cryo-EM structure of the active five-subunit Hrd1 complex (Hrd1, Hrd3, Der1, Usa1, Yos9) reveals Hrd3 and Yos9 jointly create a luminal substrate-binding site for glycosylated substrates; Hrd1 and the rhomboid-like Der1 form two 'half-channels' with opposing cavities and lateral gates in a thinned membrane region, explaining how a polypeptide loop moves through the membrane during ERAD-L.\",\n      \"method\": \"Cryo-EM of two subcomplexes, crosslinking, molecular dynamics simulation\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure combined with crosslinking and MD simulation, multiple orthogonal methods\",\n      \"pmids\": [\"32327568\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Purified Hrd1 incorporated into model membranes forms a pore whose opening is triggered by autoubiquitination; substrate binding increases pore size and activity; deubiquitination closes the pore. Two substrate-binding sites were identified: a low-affinity luminal site and a high-affinity cytoplasmic site formed after autoubiquitination of specific RING-domain lysines.\",\n      \"method\": \"Reconstitution of purified Hrd1 in model membranes, electrophysiology/pore assay, site-specific mutagenesis of RING-domain lysines\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct in vitro pore reconstitution with purified protein plus mutagenesis\",\n      \"pmids\": [\"32094691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Hrd1 autoubiquitination is counteracted by the deubiquitinating enzyme Ubp1, which requires its N-terminal transmembrane segment for activity toward Hrd1. Hrd3 acts as a brake on autoubiquitination, while Usa1 attenuates Ubp1 deubiquitination through its UBL domain, establishing a cycle of autoubiquitination/deubiquitination that gates the Hrd1 retrotranslocation channel.\",\n      \"method\": \"Genetic and biochemical analysis in S. cerevisiae, ubiquitination/deubiquitination assays, domain mutagenesis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal genetic and biochemical approaches identifying writer/eraser/regulator of Hrd1 autoubiquitination\",\n      \"pmids\": [\"31713515\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Site-specific disulfide crosslinking in live S. cerevisiae cells maps the path of a glycosylated ERAD substrate through the Hrd1 complex: the substrate contacts a groove in Hrd3 and the lectin domain of Yos9 on the luminal side, inserts a loop into the membrane with one side interacting with the Der1 lateral gate and the other with the Hrd1 lateral gate. Hrd1 autoubiquitination is required to disassemble inactive Hrd1 dimers into active monomers.\",\n      \"method\": \"Site-specific disulfide crosslinking in live cells, cryo-EM structure integration\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — site-specific crosslinking in living cells with structural integration, multiple interaction points mapped\",\n      \"pmids\": [\"35970394\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"SEL1L protein stability is critically dependent on HRD1: SEL1L is rapidly degraded when HRD1 is absent, and HRD1 co-expression stabilizes SEL1L. The endogenous HRD1-SEL1L complex (Complex I) associates with Derlin-1/2, VIMP, Herp, and OS-9, while a smaller transiently expressed complex (Complex II) lacks Derlin-1/2, VIMP, and Herp but still supports retrotranslocation.\",\n      \"method\": \"siRNA knockdown, co-immunoprecipitation, size fractionation, degradation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods, reciprocal Co-IP, functional knockdown with defined substrates\",\n      \"pmids\": [\"21454652\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Disposal of soluble ERAD-L substrates (ERAD-LS) in mammalian cells is strictly dependent on HRD1, SEL1L, and either OS-9 or XTP3-B; tethering the same substrate to the membrane (ERAD-LM) renders these factors dispensable, revealing a distinct pathway organization from yeast.\",\n      \"method\": \"siRNA knockdown with pulse-chase degradation assays, genetic epistasis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic genetic epistasis with multiple substrates and multiple ERAD components\",\n      \"pmids\": [\"20100910\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SEL1L-HRD1 interaction is required to form a functional ERAD complex: SEL1L is needed to recruit the E2 enzyme UBE2J1 and DERLIN to HRD1. A disease-causing SEL1L variant (p.Ser658Pro) reduces SEL1L stability and attenuates the SEL1L-HRD1 interaction via electrostatic repulsion between SEL1L F668 and HRD1 Y30, impairing ERAD.\",\n      \"method\": \"Biochemical analysis, proteomic interactome screens, mutagenesis, mouse model with pathogenic variant\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — proteomics, mutagenesis, and mouse pathology, multiple orthogonal methods\",\n      \"pmids\": [\"38365914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"HRD1 acts together with the E2 ubiquitin-conjugating enzyme UBE2J1 to ubiquitinate and dislocate misfolded MHC class I heavy chains from the ER. HRD1, UBE2J1, non-β2m-bound MHC I heavy chains, Derlin-1, and p97 form a complex. HRD1 discriminates misfolded MHC I from properly assembled heterotrimers.\",\n      \"method\": \"siRNA functional screen, Co-immunoprecipitation, ubiquitination assay, dislocation assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — functional siRNA screen, Co-IP complex characterization, ubiquitination assay, multiple orthogonal methods\",\n      \"pmids\": [\"21245296\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Hrd1 ubiquitinates Nrf2 and targets it for proteasomal degradation independently of the canonical Keap1 pathway. In cirrhotic livers, XBP1 transcriptionally up-regulates Hrd1, which then ubiquitinates Nrf2, suppressing the antioxidant response. Hrd1 conditional knockout mice show elevated Nrf2 levels.\",\n      \"method\": \"Hrd1 conditional knockout mouse model, ubiquitination assay, liver cirrhosis patient tissue analysis, XBP1-Hrd1 transcriptional pathway analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional knockout plus in vitro ubiquitination assay, replicated in human tissue and mouse model\",\n      \"pmids\": [\"24636985\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Hrd1 catalyzes ubiquitination and degradation of the transcriptional suppressor BLIMP1 in dendritic cells, thereby promoting MHC-II expression. Hrd1-null DCs fail to prime CD4+ T cells. Hrd1 expression is induced by TLR stimulation.\",\n      \"method\": \"Conditional Hrd1 knockout in DCs, ubiquitination assay, T cell priming assay\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — tissue-specific knockout with defined cellular phenotype, ubiquitination assay\",\n      \"pmids\": [\"25366967\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Hrd1 ubiquitinates and degrades the CDK inhibitor p27(kip1) to promote T cell proliferation; genetic deletion of Hrd1 in T cells impairs proliferation and IL-2 production, and deletion of p27(kip1) in Hrd1-null T cells rescues proliferative capacity but not cytokine production.\",\n      \"method\": \"Conditional Hrd1 knockout mouse, genetic rescue (p27 deletion), ubiquitination assay, T cell functional assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional knockout plus genetic epistasis with p27 deletion, multiple phenotypic readouts\",\n      \"pmids\": [\"27417417\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Hrd1 ubiquitinates and degrades the death receptor Fas/CD95 in B cells, protecting them from activation-induced cell death. Hrd1-null B cells exhibit elevated Fas expression during activation and undergo Fas-mediated apoptosis; Fas mutation in Hrd1 KO mice abrogates the B-cell AICD increase.\",\n      \"method\": \"Conditional Hrd1 knockout mouse, genetic rescue (Fas mutation), ubiquitination assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional knockout with genetic epistasis via Fas mutation, ubiquitination assay\",\n      \"pmids\": [\"27573825\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Sel1L-Hrd1 ERAD selectively recognizes and targets the pre-B cell receptor (pre-BCR) for proteasomal degradation in a BiP-dependent manner; loss of Sel1L-Hrd1 causes pre-BCR accumulation intracellularly and at the cell surface, leading to persistent pre-BCR signaling and developmental block at the large-to-small pre-B cell transition.\",\n      \"method\": \"Conditional Sel1L knockout in B cell precursors, pre-BCR accumulation analysis, signaling assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional knockout with defined developmental block and mechanistic pathway placement\",\n      \"pmids\": [\"27568564\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Sel1L-Hrd1 ERAD controls β cell identity by mediating the degradation of TGF-β receptor 1; Sel1L deficiency leads to loss of β cell identity (not apoptosis) that can be rescued by inhibition of TGF-β signaling, as demonstrated by single-cell RNA-seq and TGF-β receptor 1 protein accumulation.\",\n      \"method\": \"β cell-specific Sel1L conditional knockout, single-cell RNA-seq, TGF-β receptor 1 degradation assay, TGF-β pathway inhibition rescue\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — tissue-specific knockout with scRNA-seq, defined substrate, and pharmacological rescue\",\n      \"pmids\": [\"32182217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The Sel1L-Hrd1 ERAD complex controls FGF21 transcription by ubiquitinating and degrading the ER-tethered transcription factor CREBH; liver-specific Sel1L deletion elevates CREBH nuclear abundance and markedly increases circulating FGF21, establishing a hepatic ERAD-CREBH-FGF21 metabolic axis.\",\n      \"method\": \"Liver-specific Sel1L knockout mouse, CREBH ubiquitination assay, FGF21 measurement\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — tissue-specific knockout with defined substrate ubiquitination assay, replicated in two papers (PMID:30389665 and 30389664)\",\n      \"pmids\": [\"30389665\", \"30389664\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HRD1 catalyzes polyubiquitin conjugation onto CREBH at lysine K294, targeting it for proteasomal degradation in the postprandial state to downregulate FGF21 expression in liver.\",\n      \"method\": \"Liver-specific HRD1 knockout mouse, CREBH ubiquitination site mapping (K294), refeeding experiments\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — specific ubiquitination site identified, tissue-specific knockout, in vivo metabolic phenotyping\",\n      \"pmids\": [\"30389664\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The SEL1L-HRD1 ERAD complex ubiquitinates nascent STING protein and targets it for proteasomal degradation in the basal state, limiting the pool of activatable STING and thus suppressing innate immune signaling; SEL1L or HRD1 deficiency in macrophages amplifies STING-dependent antiviral and antitumor immunity.\",\n      \"method\": \"Conditional knockout in macrophages, ubiquitination assay, STING signaling assays, viral infection and tumor models\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional knockout with defined substrate, ubiquitination assay, functional immune phenotype, multiple disease models\",\n      \"pmids\": [\"37142791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"HRD1 interacts with Parkin-associated endothelin receptor-like receptor (Pael-R) through its proline-rich region, promotes Pael-R ubiquitination and degradation via the proteasome, prevents Pael-R-induced ER stress and neuronal death; ATF6 overexpression induces HRD1 and accelerates Pael-R degradation in an HRD1-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, ATF6 overexpression, neuronal cell death assay\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, ubiquitination assay, siRNA rescue, mechanistic pathway placement\",\n      \"pmids\": [\"17059562\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"HRD1 promotes ubiquitination and degradation of amyloid precursor protein (APP) through its proline-rich region interaction; suppression of HRD1 by siRNA causes APP accumulation, increased Aβ production, and ER stress; ATF6/XBP1-induced HRD1 upregulation enhances APP degradation and reduces Aβ production.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, APP and Aβ measurement\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, ubiquitination assay, siRNA, multiple readouts\",\n      \"pmids\": [\"20237263\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Hrd1 interacts with and ubiquitinates polyglutamine-expanded huntingtin N-terminal fragment (httN) in a RING-finger-dependent manner; Hrd1 recruits httN to the ER and co-localizes with juxtanuclear httN aggregates; Hrd1-mediated httN degradation is p97/VCP-dependent but Ufd1/Npl4-independent; expanded polyQ tracts are preferred substrates.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, subcellular fractionation, confocal microscopy\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, ubiquitination, siRNA, imaging, multiple orthogonal methods\",\n      \"pmids\": [\"17141218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Both Hrd1 and gp78 bind cholera toxin CTA1 and protein disulfide isomerase (PDI); dominant-negative Hrd1 or gp78 and Ube2g2 mutants decrease CTA1 retrotranslocation; CT association with Hrd1/gp78 is blocked by dominant-negative Derlin-1, suggesting a sequential handoff from Derlin-1 to Hrd1/gp78 on the ER membrane.\",\n      \"method\": \"Binding studies (Co-immunoprecipitation), dominant-negative mutant expression, retrotranslocation assay, siRNA knockdown\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional dominant-negative approach, single lab\",\n      \"pmids\": [\"19864457\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Derlin-2, but not Derlin-1 or Derlin-3, is an essential functional partner for HRD1-mediated ERAD of sonic hedgehog (SHH) and NHK substrates; without Derlin-2, HRD1 homo-oligomerization and substrate targeting proceed normally but substrates are trapped in the ER lumen, suggesting Derlin-2 regulates substrate movement through the HRD1 retrotranslocon.\",\n      \"method\": \"siRNA knockdown of individual Derlins, ERAD substrate degradation assay, retrotranslocation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic siRNA knockdown of three Derlins with functional retrotranslocation readout, multiple substrates tested\",\n      \"pmids\": [\"23867461\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"HERP proteins (HERP1/HERP2) are required for HRD1-mediated ERAD; they recruit DERL2 to the HRD1-SEL1L complex, and loss of HERPs traps substrates in the ER lumen and attenuates their ubiquitination. HERP2 is constitutively expressed whereas HERP1 is ER stress-inducible. The UBL domain of HERP1 has an additional function independent of DERL2 recruitment.\",\n      \"method\": \"siRNA knockdown, Co-immunoprecipitation, ERAD substrate degradation/retrotranslocation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple HERP paralogs tested, Co-IP, functional retrotranslocation readout\",\n      \"pmids\": [\"24366871\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Herp localizes to the ER quality control compartment (ERQC) and recruits HRD1 to this compartment; Herp is required for HRD1-mediated ubiquitination of ERAD substrates presented by OS-9 lectin at the ERQC.\",\n      \"method\": \"Confocal microscopy/live imaging, Co-immunoprecipitation, siRNA knockdown with ERAD substrate assay\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — imaging plus Co-IP and functional assay, single lab\",\n      \"pmids\": [\"24478453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Herp regulates Hrd1-mediated ubiquitylation through its ubiquitin-like (UBL) domain; the UBL domain is required for efficient ubiquitylation of the NHK ERAD substrate and for NHK degradation. Herp undergoes rapid turnover at Hrd1 complexes with multiple copies of Hrd1 per complex.\",\n      \"method\": \"Co-immunoprecipitation, UBL domain mutagenesis, ubiquitylation assay with NHK substrate\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mutagenesis plus Co-IP and functional ubiquitylation assay, single lab\",\n      \"pmids\": [\"21149444\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Affinity-tagged endogenous Hrd1 in HEK293 cells forms two distinct high-molecular-mass complexes with different interacting proteins and variable stoichiometries, indicating heterogeneity in functional Hrd1 ERAD units; complex composition is strongly influenced by Hrd1 expression levels.\",\n      \"method\": \"Genome-edited endogenous tandem affinity tag, size-exclusion chromatography, immunodepletion, absolute quantification mass spectrometry\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — endogenous tagging by genome editing plus quantitative MS, multiple biochemical fractionation methods\",\n      \"pmids\": [\"28411238\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"During ER stress, HRD1 associates with the Sec61α translocon and Derlin-1 to form a large pre-emptive quality control (ERpQC) complex; ERpQC substrates are captured by the C-terminal region of Derlin-1 and ubiquitinated by HRD1 prior to cytosolic degradation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, ER stress induction\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of trimeric complex plus ubiquitination assay, single lab\",\n      \"pmids\": [\"29743537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Grp94 uses its middle domain to interact with GABAA receptor α1 subunits in the ER lumen; OS-9 acts downstream of Grp94 to recognize misfolded α1 subunits in a glycan-dependent manner, delivering them to Hrd1-mediated ubiquitination and VCP-mediated extraction.\",\n      \"method\": \"Co-immunoprecipitation, domain mutagenesis, Grp94 inhibition, ERAD substrate assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, domain mapping, pharmacological inhibition, single lab\",\n      \"pmids\": [\"26945068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"ER stress-induced transcription of HRD1 is mediated by the IRE1-XBP1 pathway, while SEL1 induction is mediated by the ATF6-dependent pathway, revealing differential regulation of these ERAD components by distinct UPR branches.\",\n      \"method\": \"IRE1/ATF6 inhibition, XBP1 overexpression, promoter-linked induction analysis\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pathway inhibition and transcription factor overexpression, mechanistic pathway placement, single lab\",\n      \"pmids\": [\"17967421\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"USP19, an ER-anchored deubiquitinating enzyme, stabilizes HRD1 by removing K48-linked ubiquitin chains from HRD1, rescuing it from proteasomal degradation; altered USP19 expression affects steady-state HRD1 levels.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, USP19 overexpression/knockdown\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, gain/loss-of-function, single lab\",\n      \"pmids\": [\"27827840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"HRD1 is UFMylated at Lys610 by UFL1 and interacts with UFMylation components UFL1 and DDRGK1; UFL1 depletion increases HRD1 stability and reduces its ubiquitination. Mutation of HRD1 K610R impairs its ability to degrade misfolded proteins. During ER stress, UFMylation and ubiquitination of HRD1 are progressively inhibited.\",\n      \"method\": \"Co-immunoprecipitation, UFMylation assay, site-directed mutagenesis (K610R), siRNA knockdown, ERAD substrate degradation assay\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — novel PTM identified with mutagenesis and functional ERAD readout, single lab\",\n      \"pmids\": [\"37795761\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ER-localized Hrd1 directly interacts with the deubiquitinating enzyme Usp15 and inactivates its deubiquitinating activity toward IκBα (without degrading Usp15), resulting in enhanced IκBα ubiquitination and excessive NF-κB activation during TLR4-triggered bacterial infection; Hrd1 deficiency in macrophages protects mice from LPS-induced septic shock.\",\n      \"method\": \"Co-immunoprecipitation, deubiquitinase activity assay, Hrd1 knockout macrophages, septic shock mouse model, rescue with Usp15 knockdown\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, enzymatic activity assay, in vivo knockout model with rescue, multiple orthogonal methods\",\n      \"pmids\": [\"31477895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Hrd1 suppresses ER stress-induced IRE1α-p38 MAPK signaling in regulatory T cells (Tregs); genetic deletion of Hrd1 in Tregs elevates ER stress-responsive genes and IRE1α/p38 activation, destabilizing FoxP3 expression; pharmacological suppression of IRE1α kinase (but not endonuclease) activity rescues Hrd1-null Treg stability.\",\n      \"method\": \"Treg-specific Hrd1 conditional knockout, IRE1α kinase/endonuclease pharmacological inhibition, FoxP3 stability assay, multi-organ inflammation phenotype\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — cell type-specific conditional knockout, pharmacological dissection of IRE1α activities, defined FoxP3 stability readout\",\n      \"pmids\": [\"30843874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HRD1 ubiquitinates and degrades METTL14; in ER stress, accumulation of unfolded proteins competes with HRD1 to block METTL14 ubiquitination, allowing METTL14 accumulation to promote m6A modification of CHOP mRNA and reduce its translation, thereby shifting UPR toward stress adaptation over apoptosis.\",\n      \"method\": \"HRD1 ERAD machinery competition assay, METTL14 ubiquitination assay, m6A modification analysis, liver-specific METTL14 knockout\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ubiquitination assay, tissue-specific knockout, mechanistic pathway connecting ERAD to mRNA modification\",\n      \"pmids\": [\"34847358\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SYVN1/HRD1 directly interacts with GSDMD and mediates K27-linked polyubiquitination of GSDMD at K203 and K204 residues, promoting GSDMD-induced pyroptotic cell death; SYVN1 deficiency inhibits pyroptosis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay with specific ubiquitin linkage analysis, site-directed mutagenesis of GSDMD lysines, LDH/PI uptake cell death assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination site mutagenesis, functional pyroptosis assay, single lab\",\n      \"pmids\": [\"35115505\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SYVN1/HRD1 enhances degradation of the ATZ (SERPINA1 E342K) variant through SQSTM1/p62-dependent selective autophagy; SYVN1 mediates K48-linked polyubiquitination of ATZ, which is recognized by the UBA domain of SQSTM1, coupling ubiquitinated ATZ to the lysosome; autophagy inhibition attenuates SYVN1-mediated ATZ clearance.\",\n      \"method\": \"Ubiquitination assay (K48 linkage specific), autophagy inhibition/induction, Atg5 knockout cells, SQSTM1 UBA domain analysis, Co-immunoprecipitation\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — specific ubiquitin linkage analysis, genetic autophagy disruption (Atg5 KO), domain mapping, multiple orthogonal methods\",\n      \"pmids\": [\"28121484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Hrd1 interacts with tau and promotes proteasomal degradation of both total tau and phosphorylated tau through its E3 ubiquitin ligase activity; proteasome inhibition increases Hrd1-mediated tau ubiquitination; Hrd1 overexpression alleviates tau cytotoxicity.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, proteasome inhibitor treatment, cell viability assay\",\n      \"journal\": \"Current molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, siRNA, single lab\",\n      \"pmids\": [\"22280354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Hrd1 interacts with optineurin (OPTN) and promotes its proteasomal degradation and aggresome formation at the MTOC; Hrd1 overexpression increases OPTN degradation and aggresome formation, while Hrd1 knockdown stabilizes OPTN and inhibits aggresome formation; this applies to both WT and ALS/POAG mutant OPTN.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, proteasome assay, confocal microscopy of aggresome formation\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, siRNA, imaging, single lab\",\n      \"pmids\": [\"28334804\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SYVN1 (HRD1), NEDD8, and FBXO2 each contribute to ubiquitin-mediated proteasomal degradation of ΔF508-CFTR in human cystic fibrosis airway epithelia; knockdown of SYVN1, NEDD8, or FBXO2 partially restores ΔF508-CFTR-mediated Cl- transport; SYVN1 and FBXO2 represent two distinct multiprotein complexes targeting ΔF508-CFTR.\",\n      \"method\": \"siRNA knockdown in primary human airway epithelia, functional CFTR Cl- transport assay, CFTR maturation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional siRNA screen in primary human cells, two orthogonal CFTR assays, single lab\",\n      \"pmids\": [\"27756846\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Silencing of Hrd1 leads to stabilization of gp78 and a decline in gp78 ubiquitination, thereby enhancing CFTRΔf508 degradation; endogenous gp78 co-immunoprecipitates with Hrd1, and Hrd1 acts as an E3 for gp78, negatively regulating CFTRΔf508 degradation.\",\n      \"method\": \"siRNA knockdown, Co-immunoprecipitation, ubiquitination assay, cycloheximide chase\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination, siRNA, single lab\",\n      \"pmids\": [\"19828134\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HRD1 interacts with and ubiquitinates multiple metabolic enzymes including ENTPD5, CPT2, RMND1, and HSD17B4 in the liver; liver-specific HRD1 deletion elevates these proteins and hyperactivates AMPK and AKT pathways, reprogramming hepatic metabolic gene expression to suppress glycogenesis/lipogenesis and upregulate glycolysis/fatty acid oxidation.\",\n      \"method\": \"Liver-specific HRD1 knockout, proteomic interactome analysis, ubiquitination assay, genome-wide mRNA sequencing, metabolic phenotyping\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — tissue-specific knockout, proteomics interactome, functional metabolic phenotyping, multiple substrates validated\",\n      \"pmids\": [\"30201971\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"HRD1 interacts with and ubiquitinates MafA in diabetic β-cells, leading to its cytoplasmic accumulation and proteasomal degradation; HRD1 overexpression triggers impaired insulin secretion via MafA loss, while HRD1 knockdown improves glucose control in diabetic models.\",\n      \"method\": \"Proteomic analysis, Co-immunoprecipitation, ubiquitination assay, β cell-specific HRD1 overexpression and knockdown mouse models\",\n      \"journal\": \"Diabetes\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — proteomics substrate identification, Co-IP, ubiquitination assay, in vivo mouse model\",\n      \"pmids\": [\"32086291\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"HRD1 interacts with eIF2α and promotes its ubiquitylation and proteasomal degradation; HRD1 overexpression decreases phosphorylated eIF2α levels and inhibits apoptosis in renal tubular cells exposed to palmitic acid or high glucose; the protective effect of HRD1 is blunted by eIF2α overexpression.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, HRD1 overexpression/knockdown, apoptosis assay\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, rescue experiment, single lab\",\n      \"pmids\": [\"29233968\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"HRD1 interacts with IGF-1R and promotes its ubiquitination and proteasomal degradation in breast cancer cells; NF-κB/p65 binds the HRD1 promoter and inhibits HRD1 expression, explaining IL-6-induced HRD1 downregulation; HRD1 overexpression inhibits breast cancer growth and invasion in vitro and in vivo.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, promoter binding analysis, overexpression in vitro/in vivo\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, promoter analysis, single lab\",\n      \"pmids\": [\"26536657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"HRD1 interacts with and ubiquitinates SIRT2, promoting its proteasomal degradation; HRD1 deficiency induces SIRT2 upregulation and inhibits lung cancer cell growth and tumor formation both in vitro and in vivo.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, HRD1 knockdown/overexpression, tumor xenograft model\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, in vivo model, single lab\",\n      \"pmids\": [\"31932479\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HRD1 interacts with and ubiquitinates PFKP, targeting it for proteasomal degradation; HRD1-mediated PFKP degradation reduces aerobic glycolysis (Warburg effect) and inhibits breast cancer cell proliferation and invasion.\",\n      \"method\": \"Mass spectrometry HRD1 interactome, Co-immunoprecipitation, ubiquitylation assay, in vitro/in vivo tumor models\",\n      \"journal\": \"Cell communication and signaling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS interactome, Co-IP, ubiquitination assay, in vivo xenograft, single lab\",\n      \"pmids\": [\"33588886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"HRD1 interacts with CPT2 and mediates K48-linked ubiquitination of CPT2, stabilizing (not degrading) it; HRD1-mediated CPT2 stabilization inhibits fatty acid oxidation and TNBC cell proliferation under glutamine-deficient conditions.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with K48 linkage analysis, CPT2 knockdown rescue, in vivo xenograft\",\n      \"journal\": \"Molecular oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, specific ubiquitin linkage analysis, functional rescue, single lab\",\n      \"pmids\": [\"33207079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Hrd1 interacts with and ubiquitinates LOX-1, promoting its proteasomal degradation in endothelial cells; KLF2 transcription factor binds the HRD1 promoter and positively regulates HRD1 expression; loss of HRD1 causes LOX-1 accumulation and endothelial apoptosis.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, KLF2 promoter binding analysis, LOX-1 knockdown rescue\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination, promoter analysis, single lab\",\n      \"pmids\": [\"32308114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Hrd1 interacts with and ubiquitinates Acly (ATP citrate lyase), reducing its protein level and suppressing acetyl-CoA production and lipogenesis in hepatocytes; Hrd1 overexpression in db/db mice ameliorates hepatic steatosis and improves insulin sensitivity.\",\n      \"method\": \"Co-IP-based mass spectrometry, Co-immunoprecipitation, ubiquitination assay, adenovirus overexpression in db/db mice\",\n      \"journal\": \"Metabolism: clinical and experimental\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS interactome, Co-IP, ubiquitination, in vivo mouse model, single lab\",\n      \"pmids\": [\"32888949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HRD1 interacts with PTEN and promotes its ubiquitination and proteasomal degradation in hepatocellular carcinoma; HRD1 suppression inhibits HCC growth, migration, and invasion.\",\n      \"method\": \"Proteomic approach, Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, in vitro/in vivo tumor models\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination, in vivo model, single lab\",\n      \"pmids\": [\"29958993\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SYVN1/HRD1 interacts with and ubiquitinates HMGB1, promoting its degradation; SYVN1-mediated HMGB1 degradation activates the NRF2/HO-1 pathway and inhibits ferroptosis in spinal cord neurons during ischemia-reperfusion injury.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, MG132 proteasome inhibition, in vivo SCIRI rat model, adenovirus overexpression\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination, in vivo model with rescue, single lab\",\n      \"pmids\": [\"37591122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SYVN1 promotes ubiquitination and degradation of STAT3 in retinal microvascular endothelial cells; SYVN1 overexpression reduces phospho-STAT3, VEGF secretion, and neovascularization in an OIR mouse model, with effects rescued by STAT3 activator treatment.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, intravitreal adenovirus injection, retinal flatmount analysis, electroretinogram\",\n      \"journal\": \"Investigative ophthalmology & visual science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination, in vivo mouse model with pharmacological rescue, single lab\",\n      \"pmids\": [\"37540175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Exogenous H2S (NaHS) induces S-sulfhydration of Hrd1 at Cys115, enhancing Hrd1 interaction with VAMP3 and promoting VAMP3 ubiquitylation; Hrd1 C115A mutant abolishes VAMP3 ubiquitylation, CD36 membrane retention, and lipid droplet reduction in diabetic cardiomyocytes.\",\n      \"method\": \"S-sulfhydration assay, site-directed mutagenesis (C115A), Co-immunoprecipitation, LC-MS/MS ubiquitylation analysis, db/db mouse model\",\n      \"journal\": \"Aging and disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — PTM (S-sulfhydration) identified by biochemical assay with C115A mutagenesis, in vivo model, single lab\",\n      \"pmids\": [\"32257542\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"H2S-induced S-sulfhydration of Hrd1 at Cys115 enhances Hrd1 interaction with DGAT1 and DGAT2, promoting their ubiquitylation and reducing lipid droplet accumulation in diabetic cardiac tissue; Hrd1 C115A mutation abolishes this interaction and effect.\",\n      \"method\": \"S-sulfhydration assay, site-directed mutagenesis (C115A), Co-immunoprecipitation, ubiquitylation assay, db/db mouse model\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — PTM with mutagenesis validation, Co-IP, ubiquitination, in vivo model, single lab\",\n      \"pmids\": [\"34562065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Exogenous H2S promotes S-sulfhydration of Syvn1 at Cys115, facilitating Syvn1-Keap1 interaction and Keap1 ubiquitination, which activates Nrf2 nuclear translocation and the Nrf2/GPx4/GSH pathway to suppress ferroptosis in diabetic cardiomyocytes; Syvn1 C115A mutant partially attenuates these effects.\",\n      \"method\": \"S-sulfhydration assay, Syvn1 C115A mutagenesis, Co-immunoprecipitation, ubiquitination assay, db/db mouse model, Nrf2 nuclear translocation assay\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — PTM with site mutagenesis, Co-IP, in vivo model, single lab\",\n      \"pmids\": [\"37875467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SYVN1 competitively interacts with TRIM59, preventing SYVN1-mediated TRIM59 ubiquitination and stabilizing TRIM59 expression; stable TRIM59 then promotes p53 degradation, thereby inhibiting ferroptosis in pancreatic cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, competitive binding assay, in vitro and in vivo tumor models\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, competitive interaction, in vivo PDX model, single lab\",\n      \"pmids\": [\"37740007\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SYVN1 interacts with ETS1 and promotes its ubiquitination at K318, leading to proteasomal degradation of ETS1 and downregulation of xCT/SLC7A11 transcription, thereby inducing ferroptosis in breast cancer cells; a small molecule (sculponeatin A) promotes the ETS1-SYVN1 interaction to enhance this effect.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination site mapping (K318), Western blot, ferroptosis assays, in vivo mouse tumor model\",\n      \"journal\": \"Phytomedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination site mutagenesis, functional ferroptosis readout, in vivo model, single lab\",\n      \"pmids\": [\"37327642\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"HRD1 transmembrane domain transfers Pael-R from the ER to the cytosol, while the proline-rich domain is required to promote Pael-R degradation; the transmembrane domain also stabilizes HRD1 itself.\",\n      \"method\": \"Domain deletion mutagenesis, Pael-R degradation assay, HRD1 stability analysis\",\n      \"journal\": \"Journal of pharmacological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mutagenesis with functional substrate transfer and stability readouts, single lab\",\n      \"pmids\": [\"18344614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SEL1L-HRD1 ERAD degrades nascent WNT5A in a quality-control capacity; in the absence of ERAD, WNT5A misfolds and forms high-molecular-weight ER aggregates (loss of function), attenuating WNT5A-mediated suppression of hepatocyte proliferation and promoting tumorigenesis.\",\n      \"method\": \"Hepatocyte-specific Sel1L/Hrd1 knockout, proteomics substrate screen, WNT5A aggregation analysis, tumor mouse model\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — tissue-specific knockout, proteomics, WNT5A functional loss-of-function mechanism, single lab\",\n      \"pmids\": [\"36238898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SEL1L-HRD1 ERAD degrades ceruloplasmin (CP), a key ferroxidase for systemic iron distribution; in the absence of ERAD, CP accumulates in the ER, is shunted to refolding, and is secreted at elevated levels, altering systemic iron homeostasis in a manner independent of ER stress.\",\n      \"method\": \"Hepatocyte-specific Sel1L knockout, proteomics substrate screen, CP secretion assay, iron homeostasis phenotyping in mice\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — tissue-specific knockout, proteomics, mechanistic substrate analysis, single lab\",\n      \"pmids\": [\"36595688\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SEL1L-HRD1 ERAD degrades the GPI-transamidase catalytic subunit PIGK, attenuating the biogenesis of GPI-anchored proteins; disease-causing PIGK variants in inherited GPI deficiency disorders are also SEL1L-HRD1 ERAD substrates.\",\n      \"method\": \"SILAC-based quantitative proteomics with machine learning filtering, ERAD substrate validation (PIGK), GPI-anchored protein functional assay, in vitro and in vivo models\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — proteomics with stringent filtering, functional validation in multiple cell types and in vivo, disease variant analysis\",\n      \"pmids\": [\"38253565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SYVN1/HRD1 interacts with HSP90 and impacts ubiquitination of eukaryotic elongation factor 2 kinase (EEF2K) in hepatocellular carcinoma cells; SYVN1 knockdown inhibits HCC migration and invasion.\",\n      \"method\": \"Co-IP-based proteomics/mass spectrometry, immunofluorescence, Co-immunoprecipitation, ubiquitination assay\",\n      \"journal\": \"Cancer communications (London, England)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS identification, limited mechanistic follow-up of the SYVN1-HSP90-EEF2K axis, single lab\",\n      \"pmids\": [\"34196494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Hrd1 regulates collagen I maturation in renal fibrosis via the Sec23A-dependent ER-to-Golgi trafficking pathway; Hrd1 overexpression increases secreted and mature collagen I, while Hrd1 knockdown predominantly reduces mature collagen I; Sec23A knockdown blocks the Hrd1-mediated increase in collagen secretion.\",\n      \"method\": \"siRNA knockdown (Hrd1 and Sec23A), overexpression, collagen I secretion/maturation measurement, epistasis via double knockdown\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis (Sec23A-Hrd1 double knockdown), functional trafficking readout, single lab\",\n      \"pmids\": [\"24114659\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Xbp1-induced Hrd1 ubiquitinates Nrf2, leading to its degradation and reduced antioxidant response in renal tubular cells; the QSLVPDI motif on Nrf2 constitutes the active site for its interaction with Hrd1; downregulation of XBP1 reduces Hrd1 expression and enhances Nrf2/HO-1 function to protect against renal ischemia-reperfusion injury.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, XBP1 heterozygous knockout mouse, Nrf2 interaction domain mapping\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping, ubiquitination assay, in vivo mouse model, single lab\",\n      \"pmids\": [\"33654072\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SYVN1, an ERAD E3 ubiquitin ligase, promotes intra-ER degradation of GABAAα1 in the dorsal striatum; SYVN1 knockdown increases GABAAα1 protein levels within the ER; this is associated with methamphetamine-induced conditioned place preference.\",\n      \"method\": \"siRNA knockdown in primary neurons and in vivo, proteasome inhibitor treatment (MG132), subcellular (intra/extra-ER) fractionation\",\n      \"journal\": \"Frontiers in molecular neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown, subcellular fractionation, proteasome inhibition, functional behavioral readout, single lab\",\n      \"pmids\": [\"29051727\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Aβ42 oligomers enhance XBP-1s, which transcriptionally upregulates HRD1; HRD1 then acts as an endogenous downregulator of BACE1, reducing BACE1 expression and activity to lower Aβ production.\",\n      \"method\": \"XBP-1s overexpression, HRD1 knockdown, BACE1 activity assay, Aβ42 oligomer treatment\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pathway dissection with overexpression and knockdown, functional BACE1 activity assay, single lab\",\n      \"pmids\": [\"27853315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HRD1-mediated METTL14 degradation is blocked when competing unfolded/misfolded proteins accumulate during ER stress, establishing a mechanism by which protein load competes with HRD1 substrate selection to switch UPR toward adaptation.\",\n      \"method\": \"METTL14 ubiquitination competition assay, ER stress induction, liver-specific knockout\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — competition-based mechanistic assay, in vivo knockout, single lab\",\n      \"pmids\": [\"34847358\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SYVN1/HRD1 is an ER-resident multi-spanning E3 ubiquitin ligase that forms the core retrotranslocation channel of the SEL1L-HRD1 ERAD complex; its RING-H2 domain catalyzes ubiquitin transfer (working with E2 enzymes including Ubc7/UBE2J1), autoubiquitination of specific RING-domain lysines opens a ubiquitin-gated pore for luminal substrate retrotranslocation, and cycles of autoubiquitination/deubiquitination (regulated by Ubp1/USP19, Hrd3/SEL1L, and Usa1) control channel activity; the complex recruits substrates via luminal lectins OS-9/XTP3-B through the SEL1L adaptor, and coordinates with Derlin-2 and HERP proteins for membrane substrate movement; beyond canonical ERAD, HRD1 ubiquitinates a broad range of non-misfolded substrates including Nrf2, BLIMP1, p27kip1, Fas, pre-BCR, TGF-β receptor 1, STING, MafA, METTL14, GSDMD, tau, CREBH, and many metabolic enzymes, and its activity is post-translationally regulated by S-sulfhydration at Cys115 and UFMylation at Lys610.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SYVN1 (HRD1) is an ER-resident, multi-spanning E3 ubiquitin ligase that constitutes the catalytic core of the SEL1L-HRD1 ER-associated degradation (ERAD) machinery, coupling recognition of misfolded ER proteins to their ubiquitination and retrotranslocation into the cytosol for proteasomal destruction [#0, #10]. Its cytosolic RING-H2 finger binds the E2 conjugating enzymes Ubc7/UBE2J1 and is strictly required for ubiquitination of soluble and membrane misfolded substrates; the RING is also the regulatory hub of the channel [#0, #1, #12]. Reconstitution and structural work establish that HRD1 forms a membrane dimer that, upon autoubiquitination of specific RING-domain lysines, disassembles into active monomers and opens an aqueous, laterally gated pore through which substrate loops are threaded; substrate binding enlarges the pore and deubiquitination closes it, making the autoubiquitination/deubiquitination cycle the gate of retrotranslocation [#3, #4, #6, #8]. In the assembled complex HRD1 partners with SEL1L (which it reciprocally stabilizes and which recruits UBE2J1, Derlin and the luminal lectins OS-9/XTP3-B that capture glycosylated substrates), together with Der1/Derlin-2 and HERP proteins that form a second half-channel and govern substrate movement [#2, #5, #9, #11, #26, #27]. Beyond clearance of misfolded clients, HRD1 ubiquitinates a broad spectrum of folded regulatory proteins to control diverse physiology: it degrades Nrf2, BLIMP1, p27kip1, Fas, the pre-BCR, TGF-\\u03b2 receptor 1, STING, the ER-tethered transcription factor CREBH, MafA, and METTL14, thereby tuning antioxidant responses, immune-cell development and signaling, \\u03b2-cell identity, and hepatic metabolic gene programs [#13, #14, #15, #16, #17, #18, #20, #21, #38, #46]. HRD1 expression is induced by the UPR through the IRE1-XBP1 branch, and its ligase activity is itself set by post-translational modification, including S-sulfhydration at Cys115 and UFMylation at Lys610, and by deubiquitinases that stabilize it [#33, #34, #35, #57]. Disease-causing variants that weaken the SEL1L-HRD1 interaction impair ERAD, and inherited GPI-deficiency PIGK variants are themselves HRD1 substrates, linking this machinery to human Mendelian disease [#11, #65].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established that the RING-H2 motif of Der3/Hrd1p is indispensable for degrading both soluble and membrane misfolded ER proteins, defining HRD1 as a catalytic, not merely scaffolding, ERAD component.\",\n      \"evidence\": \"Site-directed RING mutagenesis (C399S), in vivo degradation and dominant-negative/genetic suppression assays in S. cerevisiae\",\n      \"pmids\": [\"10218484\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the E2 partner or biochemical mechanism\", \"Did not establish substrate recognition route\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defined HRD1 as the E3 ligase of ERAD by mapping its six-TM topology with cytosolic RING and showing direct RING-dependent binding to E2 Ubc7p and in vitro ubiquitination.\",\n      \"evidence\": \"Topology mapping, in vitro ubiquitination, Ubc7p binding, RING-mutant analysis\",\n      \"pmids\": [\"11139575\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of the channel\", \"Retrotranslocation mechanism unresolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Showed how luminal substrates reach HRD1, identifying OS-9/XTP3-B lectins that bind substrate and dock onto SEL1L via their MRH domains.\",\n      \"evidence\": \"Reciprocal Co-IP, siRNA degradation assays, domain mutagenesis in mammalian cells\",\n      \"pmids\": [\"18264092\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How lectin-bound substrate is handed to HRD1 catalysis not shown\", \"GRP94 role only correlative\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined the architecture and codependence of the mammalian complex: HRD1 stabilizes SEL1L, and disposal of soluble ERAD-L substrates strictly requires HRD1, SEL1L and OS-9/XTP3-B.\",\n      \"evidence\": \"siRNA knockdown, reciprocal Co-IP, size fractionation, pulse-chase epistasis with defined substrates\",\n      \"pmids\": [\"21454652\", \"20100910\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Distinct organization from yeast (Complex I vs II) not mechanistically explained\", \"Stoichiometry undefined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstrated that HRD1 autoubiquitination within its RING domain — not substrate ubiquitination or Cdc48 — triggers retrotranslocation of luminal domains, reordering the canonical ERAD sequence.\",\n      \"evidence\": \"Proteoliposome reconstitution with purified yeast proteins, RING-lysine mutagenesis, in vivo validation\",\n      \"pmids\": [\"27321670\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not visualize the channel\", \"Did not resolve substrate paths through the membrane\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Provided structural proof of a retrotranslocation channel, showing Hrd1 dimerizes with an eight-TM aqueous cavity and lateral gate in complex with Hrd3.\",\n      \"evidence\": \"Cryo-EM of S. cerevisiae Hrd1-Hrd3\",\n      \"pmids\": [\"28682307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Captured an inactive state\", \"Did not include Der1 half-channel or substrate\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Unified structure and function: the five-subunit complex shows Hrd1 and Der1 form two opposing half-channels in a thinned membrane while Hrd3/Yos9 build a luminal substrate site, and purified Hrd1 forms a ubiquitination-gated pore enlarged by substrate.\",\n      \"evidence\": \"Cryo-EM of subcomplexes with crosslinking and MD; pore reconstitution with electrophysiology and RING-lysine mutagenesis\",\n      \"pmids\": [\"32327568\", \"32094691\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics of dimer-to-monomer transition during catalysis not directly observed\", \"Mammalian channel structure not solved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Mapped the substrate path in living cells and showed autoubiquitination disassembles inactive Hrd1 dimers into active monomers, linking the gating cycle to oligomeric state.\",\n      \"evidence\": \"Site-specific disulfide crosslinking in live yeast integrated with cryo-EM\",\n      \"pmids\": [\"35970394\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinetics of monomer activation not quantified\", \"Generality across non-glycosylated substrates untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined the writer/eraser logic of channel gating: deubiquitinase Ubp1 reverses autoubiquitination, Hrd3 brakes it, and Usa1 attenuates Ubp1, establishing a regulated cycle.\",\n      \"evidence\": \"Genetic and biochemical ubiquitination/deubiquitination assays with domain mutagenesis in S. cerevisiae\",\n      \"pmids\": [\"31713515\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mammalian counterparts of this cycle not mapped here\", \"Quantitative balance under stress unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected complex assembly to human disease, showing SEL1L-HRD1 binding recruits UBE2J1 and DERLIN and that a pathogenic SEL1L variant disrupts the interaction by electrostatic repulsion at the SEL1L/HRD1 interface.\",\n      \"evidence\": \"Interactome proteomics, interface mutagenesis, mouse model of pathogenic variant\",\n      \"pmids\": [\"38365914\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full spectrum of affected substrates in patients not defined\", \"Other interface mutations untested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Extended HRD1 ERAD to a physiological glycoprotein, showing HRD1/UBE2J1 dislocate misfolded MHC I heavy chains while sparing assembled heterotrimers, demonstrating substrate discrimination.\",\n      \"evidence\": \"siRNA screen, Co-IP complex characterization, ubiquitination and dislocation assays\",\n      \"pmids\": [\"21245296\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of discrimination unresolved\", \"Role in antigen presentation only correlative\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed HRD1 as a regulator of folded transcription factors beyond ERAD, degrading Nrf2 (independently of Keap1) and BLIMP1 to control antioxidant responses and dendritic-cell MHC-II expression.\",\n      \"evidence\": \"Conditional knockout mice, ubiquitination assays, human tissue analysis, T-cell priming assays\",\n      \"pmids\": [\"24636985\", \"25366967\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How HRD1 recognizes cytosolic/non-ER substrates unclear\", \"Linkage to canonical ERAD machinery not established for these substrates\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Established HRD1 control of immune-cell fate by degrading p27kip1, Fas, and the pre-BCR, with genetic epistasis defining causal substrates for proliferation, survival, and developmental checkpoints.\",\n      \"evidence\": \"Conditional Hrd1/Sel1L knockouts with p27 and Fas rescue crosses, ubiquitination and signaling assays\",\n      \"pmids\": [\"27417417\", \"27573825\", \"27568564\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate selectivity mechanisms across these clients not defined\", \"Localization of these degradation events not resolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrated HRD1/SEL1L control of cell identity and innate immunity, degrading TGF-\\u03b2 receptor 1 (\\u03b2-cell identity), MafA (insulin secretion), and STING (basal antiviral tone).\",\n      \"evidence\": \"Tissue-specific knockouts/overexpression, scRNA-seq, ubiquitination assays, viral/tumor and pharmacological rescue models\",\n      \"pmids\": [\"32182217\", \"32086291\", \"37142791\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether these substrates use the retrotranslocation channel or a distinct route is unresolved\", \"Quantitative contribution relative to other ligases unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined a hepatic ERAD-CREBH-FGF21 metabolic axis and a broader metabolic-enzyme degradome (ENTPD5, CPT2, RMND1, HSD17B4), showing HRD1 ubiquitination of CREBH at K294 sets postprandial FGF21 and reprograms hepatic metabolism.\",\n      \"evidence\": \"Liver-specific knockouts, ubiquitination site mapping, refeeding studies, interactome proteomics, metabolic phenotyping\",\n      \"pmids\": [\"30389665\", \"30389664\", \"30201971\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct vs indirect effects on some metabolic enzymes not fully separated\", \"Tissue specificity of substrate set unexplained\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked HRD1 substrate selection to UPR outcome, showing accumulating misfolded proteins competitively block METTL14 degradation, raising m6A modification of CHOP mRNA to bias cells toward adaptation.\",\n      \"evidence\": \"Ubiquitination competition assays, m6A analysis, liver-specific knockouts\",\n      \"pmids\": [\"34847358\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Generality of competitive substrate triage to other clients untested\", \"Affinity hierarchy of substrates undefined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified post-translational control of HRD1 activity via UFMylation at Lys610 and discovered new quality-control substrates (PIGK in GPI biogenesis, ceruloplasmin), including disease-relevant variants.\",\n      \"evidence\": \"UFMylation and ubiquitination assays with K610R mutagenesis; SILAC proteomics with functional and in vivo substrate validation\",\n      \"pmids\": [\"37795761\", \"38253565\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Interplay between UFMylation, S-sulfhydration, and autoubiquitination not integrated\", \"Full substrate repertoire still expanding\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How HRD1 selects and engages its many non-canonical, folded cytosolic substrates relative to the structurally defined luminal retrotranslocation pathway remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model for cytosolic substrate engagement\", \"Mechanism integrating PTM regulation with substrate triage unknown\", \"Tissue-specific substrate repertoire incompletely mapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1, 3, 12]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 13, 20, 21, 38]},\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [4, 5, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [36, 44]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 4, 9, 31]},\n      {\"term_id\": \"GO:0005789\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 3, 10, 11]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [33, 38, 71]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [12, 14, 17, 21, 36]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [18, 20, 45, 53]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [3, 6, 26]}\n    ],\n    \"complexes\": [\n      \"SEL1L-HRD1 ERAD complex\",\n      \"HRD1-Hrd3-Der1-Usa1-Yos9 retrotranslocon\",\n      \"ERpQC (HRD1-Sec61\\u03b1-Derlin-1) complex\"\n    ],\n    \"partners\": [\n      \"SEL1L\",\n      \"UBE2J1\",\n      \"OS-9\",\n      \"DERL2\",\n      \"HERP\",\n      \"Hrd3\",\n      \"Yos9\",\n      \"USP15\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```","audit_flag":null,"evaluation":{"pairwise":"win"}}