{"gene":"RPN1","run_date":"2026-06-10T07:46:27","timeline":{"discoveries":[{"year":2002,"finding":"Rpn1, a base subunit of the 19S proteasome regulatory particle, directly binds the ubiquitin-like (UBL) domain of the shuttle protein Rad23 via its leucine-rich-repeat-like (LRR-like) domain, mediating delivery of ubiquitylated cargo to the proteasome.","method":"Direct binding assays; identification of Rpn1 as the UBL-binding component within the base subcomplex of the proteasome; competition experiments showing Dsk2 competes with Rad23 for the same Rpn1 LRR-like domain","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, competition experiments, domain mapping; foundational finding replicated across multiple subsequent studies","pmids":["12198498"],"is_preprint":false},{"year":2016,"finding":"Rpn1 contains two distinct functional sites within its toroid domain: site T1 recognizes ubiquitin and UBL domains (including substrate shuttling factors) with preference for K48-linked chains, and adjacent site T2 binds the UBL of deubiquitinating enzyme Ubp6 to assist in ubiquitin chain disassembly. Crystal structures of T1 with monoubiquitin and K48-diubiquitin show three neighboring outer helices engaging two ubiquitins.","method":"Crystal structure determination of Rpn1 T1 site with monoubiquitin and K48-diubiquitin; genetic identification as a sixth ubiquitin receptor; biochemical binding assays; mutagenesis","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures with functional validation, mutagenesis, multiple orthogonal methods in a single rigorous study","pmids":["26912900"],"is_preprint":false},{"year":2012,"finding":"Rpn1 harbors at least two distinct docking sites for ubiquitin-processing factors: Rad23 and Dsk2 (shuttle proteins carrying UBL domains) dock at two different receptor sites within Rpn1, whereas the deubiquitinase Ubp6 also anchors to Rpn1 but with slower dissociation kinetics, behaving as an occasional proteasome subunit. Rpn10 attaches to the central solenoid of Rpn1 and this association is stabilized by Rpn2.","method":"Binding affinity measurements (association/dissociation constants); biochemical reconstitution; pulldown assays distinguishing multiple binding sites on Rpn1","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal binding assays, kinetic measurements, independently consistent with other studies","pmids":["22318722"],"is_preprint":false},{"year":2011,"finding":"A conserved aspartic acid residue D517 in the LRR domain of Rpn1 is required for docking of the UBA-UBL shuttle protein Ddi1 (and to a lesser extent Dsk2) to the proteasome; the rpn1-D517A point mutation strongly impairs delivery of ubiquitin conjugates and blocks degradation of the Ddi1-dependent substrate Ufo1. Rad23 recruitment is not affected by this mutation, indicating distinct docking mechanisms for different shuttle proteins.","method":"Site-directed mutagenesis of Rpn1 D517; genetic suppressor screen; in vivo degradation assays for Ddi1-dependent substrate Ufo1; binding assays","journal":"BMC biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — site-directed mutagenesis combined with genetic screen and functional degradation assay, single lab but multiple orthogonal methods","pmids":["21627799"],"is_preprint":false},{"year":2019,"finding":"Phosphorylation of Rpn1 at Ser361 by PIM1/2/3 kinases promotes proper assembly of the 26S proteasome; specifically, S361-phosphorylated Rpn1 more readily forms a precursor complex with Rpt2 (an early step of 19S base assembly). The phosphatase UBLCP1 reverses this modification. Loss of S361 phosphorylation reduces proteasome activity, impairs cell proliferation, and causes oxidative stress and mitochondrial dysfunction.","method":"CRISPR/Cas9-mediated gene editing; quantitative mass spectrometry; kinome screen identifying PIM1/2/3 as writers; genetic code expansion to incorporate phosphoserine directly; co-immunoprecipitation of Rpn1-Rpt2 precursor complex","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — CRISPR editing, genetic code expansion for direct phosphoserine incorporation, quantitative MS, multiple orthogonal approaches in a single rigorous study","pmids":["31843888"],"is_preprint":false},{"year":2012,"finding":"Human Rpn1/S2 (proteasomal subunit) binds the shuttle protein NUB1L; this interaction enables proteasome-mediated degradation of FAT10-conjugated substrates. NUB1L can bind to both Rpn10 and Rpn1.","method":"Co-immunoprecipitation; yeast complementation assay; depletion of hRpn10 in human cells causing accumulation of FAT10-conjugates","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and yeast functional complementation, single lab, two orthogonal methods","pmids":["22434192"],"is_preprint":false},{"year":2002,"finding":"Structural modeling predicts that the repeat-containing domains of Rpn1 and Rpn2 adopt a novel alpha-helical toroid architecture with a central pore, positioned along the common axial pore of the ATPase hexamer to form an 'antechamber' of the 26S proteasome that may assist ATPases in unfolding protein substrates.","method":"Computational sequence analysis and molecular modeling of proteasome/cyclosome repeats; identification of strongly curved alpha-helical solenoid structural pattern","journal":"The Journal of biological chemistry","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no experimental structural validation in this paper","pmids":["12270919"],"is_preprint":false},{"year":2013,"finding":"The UBL domain of human UBLCP1 (a proteasome-associated phosphatase) interacts with the C-terminal leucine-rich repeat-like domain of Rpn1; NMR solution structure of the UBLCP1 UBL domain revealed a unique β3-α2 loop whose positively charged residues mediate this interaction.","method":"NMR solution structure determination of UBL domain; NMR binding interaction mapping with Rpn1 LRR-like domain","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR structure with binding data, single lab, no mutagenesis validation reported in abstract","pmids":["23667555"],"is_preprint":false},{"year":2017,"finding":"Using photoactivatable crosslinking polyubiquitin reagents (UbPT), Rpn1 was identified as a third proteasome ubiquitin-associating subunit (alongside Rpn10 and Rpn13) that coordinates docking of substrate shuttles, unloading of substrates, and anchoring of polyubiquitin conjugates.","method":"Synthetic photoactivatable ubiquitin crosslinking (UbPT); mass spectrometry-based interactome identification; biochemical validation","journal":"Cell chemical biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — novel chemical crosslinking tool with MS identification, single lab, orthogonal to prior genetic/biochemical evidence","pmids":["28330605"],"is_preprint":false},{"year":2021,"finding":"Rpn1 contains a second, previously uncharacterized ubiquitin/UBL-binding site located in the N-terminal section of Rpn1 (a stretch of adjacent helices), with affinities and binding preferences for polyubiquitin and UBL signals comparable to the known T1 site; binding sites on Rpn1 can be shared among Ub and UBL species, and Rpn1 and Rpn10 can compete for binding of shuttle protein Dsk2.","method":"NMR spectroscopy; photoactivatable crosslinking; mass spectrometry; mutagenesis; competition assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR, crosslinking, MS, and mutagenesis combined in a single study; multiple orthogonal methods","pmids":["34364874"],"is_preprint":false},{"year":2021,"finding":"NMR spectroscopy combined with competition assays showed that Rpn1 associates with UBL-containing proteins and polyubiquitin chains with a preference for shuttle protein Rad23, and that Rpn1 appears to contain multiple Ub/UBL-binding sites (potentially one per proteasome/cyclosome repeat), ruling out exclusive recognition sites for individual Ub/UBL signals.","method":"NMR spectroscopy; competition binding assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR and competition assays, single lab","pmids":["33617881"],"is_preprint":false},{"year":2000,"finding":"T. cruzi Rpn1 (a proteasomal regulatory-particle non-ATPase subunit 1) functionally complements the temperature-sensitive nas1 yeast mutant, rescuing growth at restrictive temperature and indicating that Rpn1 assembles into the 19S regulatory particle of the 26S proteasome.","method":"Yeast genetic complementation assay; cloning and functional expression of T. cruzi RPN1 in nas1 temperature-sensitive yeast mutant","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic complementation in yeast, single lab, single method","pmids":["11071286"],"is_preprint":false},{"year":2025,"finding":"Germ cell-specific knockout of Rpn1 (ribophorin I, a subunit of the oligosaccharyltransferase complex) in mice disrupts N-glycosylation of endoplasmic reticulum-associated proteins, inhibits meiotic progression, impairs homologous chromosome pairing, meiotic recombination, and DNA double-strand break repair, triggers ER stress, and causes male infertility.","method":"Conditional Rpn1 knockout (germ cell-specific); N-glycoproteomic profiling; functional assays for meiosis and DSB repair; ER stress markers","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean conditional KO with multiple defined phenotypic readouts and N-glycoproteomic validation, single lab","pmids":["40083683"],"is_preprint":false},{"year":2026,"finding":"RPN1 (ribophorin I) mediates post-translational N-glycosylation of PD-L1, enhancing its stability; RPN1 knockdown reduces PD-L1 glycosylation and stability, improving anti-tumor immune responses and the efficacy of anti-PD-1 therapy in triple-negative breast cancer.","method":"Co-immunoprecipitation; western blotting; flow cytometry; shRNA knockdown; in vivo tumor experiments","journal":"International journal of surgery (London, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and functional KO with defined mechanistic readout (PD-L1 glycosylation/stability), single lab","pmids":["39705151"],"is_preprint":false},{"year":2025,"finding":"CERS6 sustains RPN1 stability by inhibiting its ubiquitination; RPN1 in turn activates the IRE1-XBP1 ER stress signaling pathway, and this CERS6-RPN1-IRE1-XBP1 axis promotes ESCC cell proliferation.","method":"Co-immunoprecipitation; western blotting; ubiquitination assays; knockdown/overexpression functional experiments in vitro and in vivo","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and ubiquitination assay with functional validation, single lab","pmids":["41203639"],"is_preprint":false},{"year":2026,"finding":"A homozygous nonsense variant in RPN1 (ribophorin I) causes a congenital disorder of glycosylation; the truncated RPN1 protein destabilizes other OST complex components (STT3A, RPN2, DDOST) and eliminates a C-terminal four-helix bundle required for ribosome interaction, specifically impairing co-translational glycosylation activity of the OST-A complex while leaving OST-B-specific substrates unaffected.","method":"Patient lymphoblast biochemistry; structural modeling of OST-A and OST-B complexes; western blotting of OST complex components; substrate-specific glycosylation assays","journal":"HGG advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — structural modeling combined with biochemical validation in patient cells using substrate-specific glycosylation assays, single lab","pmids":["41935956"],"is_preprint":false}],"current_model":"RPN1 (ribophorin I/Rpn1) functions in two distinct biological contexts: as the largest subunit of the 19S proteasome regulatory particle base, where its toroid domain harbors at least two functional sites (T1 for ubiquitin/UBL recognition with K48-chain preference, T2 for Ubp6 deubiquitinase docking) that coordinate substrate recruitment, shuttle factor docking, and ubiquitin chain disassembly, with Ser361 phosphorylation by PIM kinases (reversed by UBLCP1) governing 26S proteasome assembly; and as an essential subunit of the oligosaccharyltransferase (OST) complex in the ER, where it facilitates co-translational N-glycosylation of substrate proteins (including PD-L1 stability regulation) and is required for spermatogenesis, with loss-of-function causing a congenital disorder of glycosylation by destabilizing the OST-A complex through elimination of a ribosome-interacting C-terminal four-helix bundle."},"narrative":{"mechanistic_narrative":"RPN1 (Rpn1/ribophorin I) is a multifunctional scaffold that operates in two distinct cellular machines: the 19S regulatory particle of the 26S proteasome and the endoplasmic reticulum oligosaccharyltransferase (OST) complex [PMID:12198498, PMID:41935956]. As the largest subunit of the proteasome base, its toroid/LRR-like domain serves as a major ubiquitin-receptor and docking hub, recognizing K48-linked polyubiquitin and the UBL domains of substrate shuttle factors through at least two functional sites—T1, which engages ubiquitin and UBLs and was resolved bound to mono- and K48-diubiquitin, and the adjacent T2, which docks the deubiquitinase Ubp6 to support ubiquitin chain disassembly [PMID:26912900, PMID:28330605]. Distinct surfaces on Rpn1 discriminate among shuttle proteins: Rad23 and Dsk2 dock at separate receptor sites, the conserved residue D517 is specifically required for Ddi1 docking and degradation of Ddi1-dependent substrates, and the human ortholog binds the FAT10-pathway shuttle NUB1L [PMID:22318722, PMID:21627799, PMID:22434192], with additional N-terminal ubiquitin/UBL-binding capacity establishing Rpn1 as a multivalent recruitment platform [PMID:34364874, PMID:33617881]. Proteasome assembly is regulated by phosphorylation of Ser361 by PIM1/2/3 kinases, which promotes formation of the Rpn1–Rpt2 base precursor and is reversed by the proteasome phosphatase UBLCP1, whose UBL domain binds the Rpn1 LRR-like domain [PMID:31843888, PMID:23667555]. In its second role, RPN1 is an essential subunit of the OST-A complex that carries out co-translational N-glycosylation; its C-terminal four-helix bundle mediates ribosome interaction, and a homozygous nonsense variant that truncates this region destabilizes STT3A, RPN2 and DDOST and causes a congenital disorder of glycosylation [PMID:41935956]. Through OST-dependent glycosylation RPN1 supports spermatogenesis and meiotic progression and stabilizes glycoprotein substrates including PD-L1 [PMID:40083683, PMID:39705151].","teleology":[{"year":2000,"claim":"Established that Rpn1 is a bona fide structural component of the 19S regulatory particle of the 26S proteasome, anchoring all subsequent functional study to a defined assembly.","evidence":"Functional complementation of the temperature-sensitive yeast nas1 mutant by T. cruzi RPN1","pmids":["11071286"],"confidence":"Medium","gaps":["Single complementation method; no direct biochemical role assigned","Does not address ubiquitin-recognition or OST functions"]},{"year":2002,"claim":"Identified Rpn1 as the proteasome subcomponent that receives ubiquitylated cargo, answering how shuttle factors deliver substrates to the base.","evidence":"Direct binding and competition assays showing Rad23/Dsk2 UBL docking on the Rpn1 LRR-like domain; structural modeling of an Rpn1/Rpn2 toroid antechamber","pmids":["12198498","12270919"],"confidence":"High","gaps":["Toroid antechamber model was computational only","Atomic basis of UBL recognition not yet defined"]},{"year":2011,"claim":"Defined shuttle-specific docking determinants, showing different UBL carriers use distinct Rpn1 surfaces rather than a single generic receptor.","evidence":"Site-directed mutagenesis (D517A), genetic suppressor screen, and in vivo degradation of the Ddi1-dependent substrate Ufo1","pmids":["21627799"],"confidence":"High","gaps":["Single lab; structural footprint of Ddi1 docking not resolved","Whether D517 contributes to other shuttle interactions unclear"]},{"year":2012,"claim":"Resolved the multivalent docking architecture of Rpn1 and extended its receptor role to the FAT10 pathway.","evidence":"Kinetic binding/affinity measurements distinguishing Rad23, Dsk2 and Ubp6 sites; Co-IP and yeast complementation linking hRpn1 to NUB1L-mediated FAT10 degradation","pmids":["22318722","22434192"],"confidence":"Medium","gaps":["NUB1L interaction shown without reciprocal structural mapping","Hierarchy among competing factors in vivo not established"]},{"year":2016,"claim":"Provided the atomic basis for Rpn1 as a ubiquitin receptor, defining the T1 and T2 functional sites and a K48-chain preference.","evidence":"Crystal structures of T1 with monoubiquitin and K48-diubiquitin plus genetic and mutagenesis validation; T2 identified as the Ubp6 docking site","pmids":["26912900"],"confidence":"High","gaps":["Did not enumerate all binding sites on the solenoid","Dynamics of substrate hand-off to ATPases unresolved"]},{"year":2017,"claim":"Confirmed in a native context that Rpn1 is a third intrinsic proteasome ubiquitin receptor alongside Rpn10 and Rpn13.","evidence":"Photoactivatable polyubiquitin crosslinking (UbPT) with MS-based interactome identification","pmids":["28330605"],"confidence":"Medium","gaps":["Single chemical-tool approach","Quantitative contribution relative to Rpn10/Rpn13 not partitioned"]},{"year":2019,"claim":"Uncovered phospho-regulation of proteasome assembly through Rpn1, linking a kinase/phosphatase pair to base biogenesis and cellular fitness.","evidence":"CRISPR editing, kinome screen, genetic-code-expansion phosphoserine incorporation, quantitative MS, and Co-IP of the Rpn1-Rpt2 precursor; UBLCP1 as the opposing phosphatase","pmids":["31843888"],"confidence":"High","gaps":["Upstream signals controlling PIM activity on Rpn1 unknown","Whether phosphorylation also affects ubiquitin recognition not tested"]},{"year":2021,"claim":"Expanded the receptor model to multiple Ub/UBL-binding sites along Rpn1, including a new N-terminal site, and showed competition with Rpn10 for shuttles.","evidence":"NMR spectroscopy, photoactivatable crosslinking, MS, mutagenesis, and competition assays","pmids":["34364874","33617881"],"confidence":"High","gaps":["Whether each repeat truly forms a functional site in vivo unresolved","Functional consequence of inter-receptor competition for degradation kinetics unclear"]},{"year":2025,"claim":"Established the physiological importance of RPN1's OST function, linking N-glycosylation to meiosis and male fertility.","evidence":"Germ cell-specific conditional Rpn1 knockout in mice with N-glycoproteomics and meiotic/DSB-repair phenotyping","pmids":["40083683"],"confidence":"Medium","gaps":["Specific glycoprotein substrates driving meiotic defects not pinpointed","Single lab; relationship to proteasomal role not addressed"]},{"year":2026,"claim":"Defined RPN1 as causative for a congenital disorder of glycosylation and pinpointed its C-terminal ribosome-interacting bundle as essential for OST-A activity.","evidence":"Patient lymphoblast biochemistry, OST structural modeling, and substrate-specific glycosylation assays showing OST-A-selective impairment and destabilization of STT3A/RPN2/DDOST","pmids":["41935956","39705151","41203639"],"confidence":"Medium","gaps":["Single patient/single lab for the disease variant","Mechanistic interplay between OST-A destabilization and downstream glycoprotein clients incompletely mapped"]},{"year":null,"claim":"How RPN1's proteasomal and OST roles are coordinated within a cell, and how its multiple ubiquitin/UBL receptor sites are prioritized during substrate processing, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model connecting proteasome-base and ER-OST functions","Substrate selection logic among competing receptor sites unknown","In vivo dynamics of shuttle hand-off to the ATPase ring not resolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[0,1,2,8,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,3,8]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[12,13,15]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[11,15]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[12,15]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,12,15]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,8,9]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[4,12,14]}],"complexes":["19S proteasome regulatory particle (base)","26S proteasome","oligosaccharyltransferase (OST-A) complex"],"partners":["RAD23","DSK2","DDI1","UBP6","RPT2","UBLCP1","NUB1L","STT3A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P04843","full_name":"Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1","aliases":["Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunit","Ribophorin I","RPN-I","Ribophorin-1"],"length_aa":607,"mass_kda":68.6,"function":"Subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation (PubMed:31831667). N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity (By similarity)","subcellular_location":"Endoplasmic reticulum membrane; Melanosome","url":"https://www.uniprot.org/uniprotkb/P04843/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPN1","classification":"Common Essential","n_dependent_lines":1180,"n_total_lines":1208,"dependency_fraction":0.9768211920529801},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000163902","cell_line_id":"CID000183","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"DAD1","stoichiometry":10.0},{"gene":"DDOST","stoichiometry":10.0},{"gene":"KRTCAP2","stoichiometry":10.0},{"gene":"RPN2","stoichiometry":10.0},{"gene":"MLEC","stoichiometry":10.0},{"gene":"CANX","stoichiometry":4.0},{"gene":"TMPO","stoichiometry":4.0},{"gene":"EMD","stoichiometry":4.0},{"gene":"POR","stoichiometry":4.0},{"gene":"MAGT1","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000183","total_profiled":1310},"omim":[{"mim_id":"620870","title":"DNA DAMAGE-INDUCIBLE 1 HOMOLOG 1; DDI1","url":"https://www.omim.org/entry/620870"},{"mim_id":"619029","title":"KERATINOCYTE-ASSOCIATED PROTEIN 2; KRTCAP2","url":"https://www.omim.org/entry/619029"},{"mim_id":"618932","title":"OLIGOSACCHARYLTRANSFERASE COMPLEX, SUBUNIT 4, NONCATALYTIC; OST4","url":"https://www.omim.org/entry/618932"},{"mim_id":"613777","title":"FAD-DEPENDENT OXIDOREDUCTASE DOMAIN-CONTAINING PROTEIN 2; FOXRED2","url":"https://www.omim.org/entry/613777"},{"mim_id":"608605","title":"OLIGOSACCHARYLTRANSFERASE COMPLEX, CATALYTIC SUBUNIT STT3B; STT3B","url":"https://www.omim.org/entry/608605"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Endoplasmic reticulum","reliability":"Enhanced"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPN1"},"hgnc":{"alias_symbol":["OST1"],"prev_symbol":[]},"alphafold":{"accession":"P04843","domains":[{"cath_id":"2.60.40.1730","chopping":"32-220","consensus_level":"high","plddt":93.1937,"start":32,"end":220},{"cath_id":"2.60.40.1730","chopping":"226-437","consensus_level":"high","plddt":94.7222,"start":226,"end":437},{"cath_id":"-","chopping":"468-607","consensus_level":"high","plddt":90.7685,"start":468,"end":607}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P04843","model_url":"https://alphafold.ebi.ac.uk/files/AF-P04843-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P04843-F1-predicted_aligned_error_v6.png","plddt_mean":90.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPN1","jax_strain_url":"https://www.jax.org/strain/search?query=RPN1"},"sequence":{"accession":"P04843","fasta_url":"https://rest.uniprot.org/uniprotkb/P04843.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P04843/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P04843"}},"corpus_meta":[{"pmid":"12198498","id":"PMC_12198498","title":"Proteasome subunit Rpn1 binds ubiquitin-like protein domains.","date":"2002","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/12198498","citation_count":375,"is_preprint":false},{"pmid":"22689970","id":"PMC_22689970","title":"Reconstitution of abscisic acid activation of SLAC1 anion channel by CPK6 and OST1 kinases and branched ABI1 PP2C phosphatase action.","date":"2012","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/22689970","citation_count":341,"is_preprint":false},{"pmid":"19785574","id":"PMC_19785574","title":"Threonine at position 306 of the KAT1 potassium channel is essential for channel activity and is a target site for ABA-activated SnRK2/OST1/SnRK2.6 protein kinase.","date":"2009","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/19785574","citation_count":255,"is_preprint":false},{"pmid":"26912900","id":"PMC_26912900","title":"Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome.","date":"2016","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/26912900","citation_count":253,"is_preprint":false},{"pmid":"25550508","id":"PMC_25550508","title":"Nitric oxide negatively regulates abscisic acid signaling in guard cells by S-nitrosylation of OST1.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25550508","citation_count":242,"is_preprint":false},{"pmid":"26163575","id":"PMC_26163575","title":"Aquaporins Contribute to ABA-Triggered Stomatal Closure through OST1-Mediated Phosphorylation.","date":"2015","source":"The Plant cell","url":"https://pubmed.ncbi.nlm.nih.gov/26163575","citation_count":232,"is_preprint":false},{"pmid":"20128877","id":"PMC_20128877","title":"Ozone-triggered rapid stomatal response involves the production of reactive oxygen species, and is controlled by SLAC1 and OST1.","date":"2010","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/20128877","citation_count":205,"is_preprint":false},{"pmid":"16766677","id":"PMC_16766677","title":"Identification of features regulating OST1 kinase activity and OST1 function in guard cells.","date":"2006","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/16766677","citation_count":189,"is_preprint":false},{"pmid":"21423149","id":"PMC_21423149","title":"Central functions of bicarbonate in S-type anion channel activation and OST1 protein kinase in CO2 signal transduction in guard cell.","date":"2011","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/21423149","citation_count":157,"is_preprint":false},{"pmid":"29507081","id":"PMC_29507081","title":"OST1-mediated BTF3L phosphorylation positively regulates CBFs during plant cold responses.","date":"2018","source":"The EMBO 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identification of Rpn1 as the UBL-binding component within the base subcomplex of the proteasome; competition experiments showing Dsk2 competes with Rad23 for the same Rpn1 LRR-like domain\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, competition experiments, domain mapping; foundational finding replicated across multiple subsequent studies\",\n      \"pmids\": [\"12198498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Rpn1 contains two distinct functional sites within its toroid domain: site T1 recognizes ubiquitin and UBL domains (including substrate shuttling factors) with preference for K48-linked chains, and adjacent site T2 binds the UBL of deubiquitinating enzyme Ubp6 to assist in ubiquitin chain disassembly. Crystal structures of T1 with monoubiquitin and K48-diubiquitin show three neighboring outer helices engaging two ubiquitins.\",\n      \"method\": \"Crystal structure determination of Rpn1 T1 site with monoubiquitin and K48-diubiquitin; genetic identification as a sixth ubiquitin receptor; biochemical binding assays; mutagenesis\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures with functional validation, mutagenesis, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"26912900\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Rpn1 harbors at least two distinct docking sites for ubiquitin-processing factors: Rad23 and Dsk2 (shuttle proteins carrying UBL domains) dock at two different receptor sites within Rpn1, whereas the deubiquitinase Ubp6 also anchors to Rpn1 but with slower dissociation kinetics, behaving as an occasional proteasome subunit. Rpn10 attaches to the central solenoid of Rpn1 and this association is stabilized by Rpn2.\",\n      \"method\": \"Binding affinity measurements (association/dissociation constants); biochemical reconstitution; pulldown assays distinguishing multiple binding sites on Rpn1\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal binding assays, kinetic measurements, independently consistent with other studies\",\n      \"pmids\": [\"22318722\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"A conserved aspartic acid residue D517 in the LRR domain of Rpn1 is required for docking of the UBA-UBL shuttle protein Ddi1 (and to a lesser extent Dsk2) to the proteasome; the rpn1-D517A point mutation strongly impairs delivery of ubiquitin conjugates and blocks degradation of the Ddi1-dependent substrate Ufo1. Rad23 recruitment is not affected by this mutation, indicating distinct docking mechanisms for different shuttle proteins.\",\n      \"method\": \"Site-directed mutagenesis of Rpn1 D517; genetic suppressor screen; in vivo degradation assays for Ddi1-dependent substrate Ufo1; binding assays\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — site-directed mutagenesis combined with genetic screen and functional degradation assay, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"21627799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Phosphorylation of Rpn1 at Ser361 by PIM1/2/3 kinases promotes proper assembly of the 26S proteasome; specifically, S361-phosphorylated Rpn1 more readily forms a precursor complex with Rpt2 (an early step of 19S base assembly). The phosphatase UBLCP1 reverses this modification. Loss of S361 phosphorylation reduces proteasome activity, impairs cell proliferation, and causes oxidative stress and mitochondrial dysfunction.\",\n      \"method\": \"CRISPR/Cas9-mediated gene editing; quantitative mass spectrometry; kinome screen identifying PIM1/2/3 as writers; genetic code expansion to incorporate phosphoserine directly; co-immunoprecipitation of Rpn1-Rpt2 precursor complex\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — CRISPR editing, genetic code expansion for direct phosphoserine incorporation, quantitative MS, multiple orthogonal approaches in a single rigorous study\",\n      \"pmids\": [\"31843888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Human Rpn1/S2 (proteasomal subunit) binds the shuttle protein NUB1L; this interaction enables proteasome-mediated degradation of FAT10-conjugated substrates. NUB1L can bind to both Rpn10 and Rpn1.\",\n      \"method\": \"Co-immunoprecipitation; yeast complementation assay; depletion of hRpn10 in human cells causing accumulation of FAT10-conjugates\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and yeast functional complementation, single lab, two orthogonal methods\",\n      \"pmids\": [\"22434192\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Structural modeling predicts that the repeat-containing domains of Rpn1 and Rpn2 adopt a novel alpha-helical toroid architecture with a central pore, positioned along the common axial pore of the ATPase hexamer to form an 'antechamber' of the 26S proteasome that may assist ATPases in unfolding protein substrates.\",\n      \"method\": \"Computational sequence analysis and molecular modeling of proteasome/cyclosome repeats; identification of strongly curved alpha-helical solenoid structural pattern\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no experimental structural validation in this paper\",\n      \"pmids\": [\"12270919\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The UBL domain of human UBLCP1 (a proteasome-associated phosphatase) interacts with the C-terminal leucine-rich repeat-like domain of Rpn1; NMR solution structure of the UBLCP1 UBL domain revealed a unique β3-α2 loop whose positively charged residues mediate this interaction.\",\n      \"method\": \"NMR solution structure determination of UBL domain; NMR binding interaction mapping with Rpn1 LRR-like domain\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR structure with binding data, single lab, no mutagenesis validation reported in abstract\",\n      \"pmids\": [\"23667555\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Using photoactivatable crosslinking polyubiquitin reagents (UbPT), Rpn1 was identified as a third proteasome ubiquitin-associating subunit (alongside Rpn10 and Rpn13) that coordinates docking of substrate shuttles, unloading of substrates, and anchoring of polyubiquitin conjugates.\",\n      \"method\": \"Synthetic photoactivatable ubiquitin crosslinking (UbPT); mass spectrometry-based interactome identification; biochemical validation\",\n      \"journal\": \"Cell chemical biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — novel chemical crosslinking tool with MS identification, single lab, orthogonal to prior genetic/biochemical evidence\",\n      \"pmids\": [\"28330605\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Rpn1 contains a second, previously uncharacterized ubiquitin/UBL-binding site located in the N-terminal section of Rpn1 (a stretch of adjacent helices), with affinities and binding preferences for polyubiquitin and UBL signals comparable to the known T1 site; binding sites on Rpn1 can be shared among Ub and UBL species, and Rpn1 and Rpn10 can compete for binding of shuttle protein Dsk2.\",\n      \"method\": \"NMR spectroscopy; photoactivatable crosslinking; mass spectrometry; mutagenesis; competition assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR, crosslinking, MS, and mutagenesis combined in a single study; multiple orthogonal methods\",\n      \"pmids\": [\"34364874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NMR spectroscopy combined with competition assays showed that Rpn1 associates with UBL-containing proteins and polyubiquitin chains with a preference for shuttle protein Rad23, and that Rpn1 appears to contain multiple Ub/UBL-binding sites (potentially one per proteasome/cyclosome repeat), ruling out exclusive recognition sites for individual Ub/UBL signals.\",\n      \"method\": \"NMR spectroscopy; competition binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR and competition assays, single lab\",\n      \"pmids\": [\"33617881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"T. cruzi Rpn1 (a proteasomal regulatory-particle non-ATPase subunit 1) functionally complements the temperature-sensitive nas1 yeast mutant, rescuing growth at restrictive temperature and indicating that Rpn1 assembles into the 19S regulatory particle of the 26S proteasome.\",\n      \"method\": \"Yeast genetic complementation assay; cloning and functional expression of T. cruzi RPN1 in nas1 temperature-sensitive yeast mutant\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic complementation in yeast, single lab, single method\",\n      \"pmids\": [\"11071286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Germ cell-specific knockout of Rpn1 (ribophorin I, a subunit of the oligosaccharyltransferase complex) in mice disrupts N-glycosylation of endoplasmic reticulum-associated proteins, inhibits meiotic progression, impairs homologous chromosome pairing, meiotic recombination, and DNA double-strand break repair, triggers ER stress, and causes male infertility.\",\n      \"method\": \"Conditional Rpn1 knockout (germ cell-specific); N-glycoproteomic profiling; functional assays for meiosis and DSB repair; ER stress markers\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean conditional KO with multiple defined phenotypic readouts and N-glycoproteomic validation, single lab\",\n      \"pmids\": [\"40083683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"RPN1 (ribophorin I) mediates post-translational N-glycosylation of PD-L1, enhancing its stability; RPN1 knockdown reduces PD-L1 glycosylation and stability, improving anti-tumor immune responses and the efficacy of anti-PD-1 therapy in triple-negative breast cancer.\",\n      \"method\": \"Co-immunoprecipitation; western blotting; flow cytometry; shRNA knockdown; in vivo tumor experiments\",\n      \"journal\": \"International journal of surgery (London, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and functional KO with defined mechanistic readout (PD-L1 glycosylation/stability), single lab\",\n      \"pmids\": [\"39705151\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CERS6 sustains RPN1 stability by inhibiting its ubiquitination; RPN1 in turn activates the IRE1-XBP1 ER stress signaling pathway, and this CERS6-RPN1-IRE1-XBP1 axis promotes ESCC cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation; western blotting; ubiquitination assays; knockdown/overexpression functional experiments in vitro and in vivo\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and ubiquitination assay with functional validation, single lab\",\n      \"pmids\": [\"41203639\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"A homozygous nonsense variant in RPN1 (ribophorin I) causes a congenital disorder of glycosylation; the truncated RPN1 protein destabilizes other OST complex components (STT3A, RPN2, DDOST) and eliminates a C-terminal four-helix bundle required for ribosome interaction, specifically impairing co-translational glycosylation activity of the OST-A complex while leaving OST-B-specific substrates unaffected.\",\n      \"method\": \"Patient lymphoblast biochemistry; structural modeling of OST-A and OST-B complexes; western blotting of OST complex components; substrate-specific glycosylation assays\",\n      \"journal\": \"HGG advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structural modeling combined with biochemical validation in patient cells using substrate-specific glycosylation assays, single lab\",\n      \"pmids\": [\"41935956\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPN1 (ribophorin I/Rpn1) functions in two distinct biological contexts: as the largest subunit of the 19S proteasome regulatory particle base, where its toroid domain harbors at least two functional sites (T1 for ubiquitin/UBL recognition with K48-chain preference, T2 for Ubp6 deubiquitinase docking) that coordinate substrate recruitment, shuttle factor docking, and ubiquitin chain disassembly, with Ser361 phosphorylation by PIM kinases (reversed by UBLCP1) governing 26S proteasome assembly; and as an essential subunit of the oligosaccharyltransferase (OST) complex in the ER, where it facilitates co-translational N-glycosylation of substrate proteins (including PD-L1 stability regulation) and is required for spermatogenesis, with loss-of-function causing a congenital disorder of glycosylation by destabilizing the OST-A complex through elimination of a ribosome-interacting C-terminal four-helix bundle.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPN1 (Rpn1/ribophorin I) is a multifunctional scaffold that operates in two distinct cellular machines: the 19S regulatory particle of the 26S proteasome and the endoplasmic reticulum oligosaccharyltransferase (OST) complex [#0, #15]. As the largest subunit of the proteasome base, its toroid/LRR-like domain serves as a major ubiquitin-receptor and docking hub, recognizing K48-linked polyubiquitin and the UBL domains of substrate shuttle factors through at least two functional sites—T1, which engages ubiquitin and UBLs and was resolved bound to mono- and K48-diubiquitin, and the adjacent T2, which docks the deubiquitinase Ubp6 to support ubiquitin chain disassembly [#1, #8]. Distinct surfaces on Rpn1 discriminate among shuttle proteins: Rad23 and Dsk2 dock at separate receptor sites, the conserved residue D517 is specifically required for Ddi1 docking and degradation of Ddi1-dependent substrates, and the human ortholog binds the FAT10-pathway shuttle NUB1L [#2, #3, #5], with additional N-terminal ubiquitin/UBL-binding capacity establishing Rpn1 as a multivalent recruitment platform [#9, #10]. Proteasome assembly is regulated by phosphorylation of Ser361 by PIM1/2/3 kinases, which promotes formation of the Rpn1–Rpt2 base precursor and is reversed by the proteasome phosphatase UBLCP1, whose UBL domain binds the Rpn1 LRR-like domain [#4, #7]. In its second role, RPN1 is an essential subunit of the OST-A complex that carries out co-translational N-glycosylation; its C-terminal four-helix bundle mediates ribosome interaction, and a homozygous nonsense variant that truncates this region destabilizes STT3A, RPN2 and DDOST and causes a congenital disorder of glycosylation [#15]. Through OST-dependent glycosylation RPN1 supports spermatogenesis and meiotic progression and stabilizes glycoprotein substrates including PD-L1 [#12, #13].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established that Rpn1 is a bona fide structural component of the 19S regulatory particle of the 26S proteasome, anchoring all subsequent functional study to a defined assembly.\",\n      \"evidence\": \"Functional complementation of the temperature-sensitive yeast nas1 mutant by T. cruzi RPN1\",\n      \"pmids\": [\"11071286\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single complementation method; no direct biochemical role assigned\", \"Does not address ubiquitin-recognition or OST functions\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Identified Rpn1 as the proteasome subcomponent that receives ubiquitylated cargo, answering how shuttle factors deliver substrates to the base.\",\n      \"evidence\": \"Direct binding and competition assays showing Rad23/Dsk2 UBL docking on the Rpn1 LRR-like domain; structural modeling of an Rpn1/Rpn2 toroid antechamber\",\n      \"pmids\": [\"12198498\", \"12270919\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Toroid antechamber model was computational only\", \"Atomic basis of UBL recognition not yet defined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defined shuttle-specific docking determinants, showing different UBL carriers use distinct Rpn1 surfaces rather than a single generic receptor.\",\n      \"evidence\": \"Site-directed mutagenesis (D517A), genetic suppressor screen, and in vivo degradation of the Ddi1-dependent substrate Ufo1\",\n      \"pmids\": [\"21627799\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single lab; structural footprint of Ddi1 docking not resolved\", \"Whether D517 contributes to other shuttle interactions unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Resolved the multivalent docking architecture of Rpn1 and extended its receptor role to the FAT10 pathway.\",\n      \"evidence\": \"Kinetic binding/affinity measurements distinguishing Rad23, Dsk2 and Ubp6 sites; Co-IP and yeast complementation linking hRpn1 to NUB1L-mediated FAT10 degradation\",\n      \"pmids\": [\"22318722\", \"22434192\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"NUB1L interaction shown without reciprocal structural mapping\", \"Hierarchy among competing factors in vivo not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Provided the atomic basis for Rpn1 as a ubiquitin receptor, defining the T1 and T2 functional sites and a K48-chain preference.\",\n      \"evidence\": \"Crystal structures of T1 with monoubiquitin and K48-diubiquitin plus genetic and mutagenesis validation; T2 identified as the Ubp6 docking site\",\n      \"pmids\": [\"26912900\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Did not enumerate all binding sites on the solenoid\", \"Dynamics of substrate hand-off to ATPases unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Confirmed in a native context that Rpn1 is a third intrinsic proteasome ubiquitin receptor alongside Rpn10 and Rpn13.\",\n      \"evidence\": \"Photoactivatable polyubiquitin crosslinking (UbPT) with MS-based interactome identification\",\n      \"pmids\": [\"28330605\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single chemical-tool approach\", \"Quantitative contribution relative to Rpn10/Rpn13 not partitioned\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Uncovered phospho-regulation of proteasome assembly through Rpn1, linking a kinase/phosphatase pair to base biogenesis and cellular fitness.\",\n      \"evidence\": \"CRISPR editing, kinome screen, genetic-code-expansion phosphoserine incorporation, quantitative MS, and Co-IP of the Rpn1-Rpt2 precursor; UBLCP1 as the opposing phosphatase\",\n      \"pmids\": [\"31843888\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Upstream signals controlling PIM activity on Rpn1 unknown\", \"Whether phosphorylation also affects ubiquitin recognition not tested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Expanded the receptor model to multiple Ub/UBL-binding sites along Rpn1, including a new N-terminal site, and showed competition with Rpn10 for shuttles.\",\n      \"evidence\": \"NMR spectroscopy, photoactivatable crosslinking, MS, mutagenesis, and competition assays\",\n      \"pmids\": [\"34364874\", \"33617881\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Whether each repeat truly forms a functional site in vivo unresolved\", \"Functional consequence of inter-receptor competition for degradation kinetics unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established the physiological importance of RPN1's OST function, linking N-glycosylation to meiosis and male fertility.\",\n      \"evidence\": \"Germ cell-specific conditional Rpn1 knockout in mice with N-glycoproteomics and meiotic/DSB-repair phenotyping\",\n      \"pmids\": [\"40083683\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Specific glycoprotein substrates driving meiotic defects not pinpointed\", \"Single lab; relationship to proteasomal role not addressed\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined RPN1 as causative for a congenital disorder of glycosylation and pinpointed its C-terminal ribosome-interacting bundle as essential for OST-A activity.\",\n      \"evidence\": \"Patient lymphoblast biochemistry, OST structural modeling, and substrate-specific glycosylation assays showing OST-A-selective impairment and destabilization of STT3A/RPN2/DDOST\",\n      \"pmids\": [\"41935956\", \"39705151\", \"41203639\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single patient/single lab for the disease variant\", \"Mechanistic interplay between OST-A destabilization and downstream glycoprotein clients incompletely mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RPN1's proteasomal and OST roles are coordinated within a cell, and how its multiple ubiquitin/UBL receptor sites are prioritized during substrate processing, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No unified model connecting proteasome-base and ER-OST functions\", \"Substrate selection logic among competing receptor sites unknown\", \"In vivo dynamics of shuttle hand-off to the ATPase ring not resolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [0, 1, 2, 8, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 3, 8]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [12, 13, 15]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [11, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [12, 15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 12, 15]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 8, 9]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [4, 12, 14]}\n    ],\n    \"complexes\": [\n      \"19S proteasome regulatory particle (base)\",\n      \"26S proteasome\",\n      \"oligosaccharyltransferase (OST-A) complex\"\n    ],\n    \"partners\": [\n      \"Rad23\",\n      \"Dsk2\",\n      \"Ddi1\",\n      \"Ubp6\",\n      \"Rpt2\",\n      \"UBLCP1\",\n      \"NUB1L\",\n      \"STT3A\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}