{"gene":"DNAJB11","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2000,"finding":"HEDJ/DNAJB11 is a luminal, membrane-associated ER-resident Hsp40 co-chaperone whose J domain interacts with the ER-associated Hsp70 BiP in an ATP-dependent manner and stimulates BiP's ATPase activity in vitro.","method":"Confocal microscopy for ER localization; protease susceptibility, glycosidase treatment, detergent solubility assays for luminal orientation; in vitro ATPase stimulation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal biochemical methods (localization, topology, in vitro ATPase assay) in a single study; replicated by subsequent work","pmids":["10827079"],"is_preprint":false},{"year":2004,"finding":"ERdj3 directly binds unfolded protein substrates (unassembled Ig heavy chains, unfolded light chains, VSV-G ts045 mutant) independently of BiP; an ERdj3 mutant unable to stimulate BiP's ATPase activity in vitro or bind BiP in vivo retains substrate binding, indicating ERdj3 contacts substrates directly rather than via BiP. ERdj3 binds substrates first and dissociates before folding is complete, whereas BiP remains bound longer, supporting a model where ERdj3 inhibits aggregation until BiP joins and then BiP-interaction triggers ERdj3 release.","method":"In vitro ATPase stimulation assay; co-immunoprecipitation; ERdj3 ATPase-stimulation-dead mutant; pulse-chase kinetics","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro mutagenesis combined with in vivo co-IP; mechanistic model supported by multiple orthogonal experiments; replicated in subsequent studies","pmids":["15525676"],"is_preprint":false},{"year":2004,"finding":"ERdj3 is moderately induced by ER stressors; siRNA-mediated reduction of ERdj3 decreases ER stress tolerance in neuroblastoma cells, while overexpression of ERdj3 suppresses vero toxin-induced cell death.","method":"siRNA knockdown; ERdj3 overexpression by gene transfection; cell viability assays","journal":"Cell stress & chaperones","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — clean KD/KO with defined phenotypic readout, single lab","pmids":["15544163"],"is_preprint":false},{"year":2005,"finding":"Within the ER lumen, Shiga toxin interacts with HEDJ/ERdj3 and is found in a complex containing HEDJ and the translocon Sec61, suggesting ERdj3 participates in retrotranslocation of Shiga toxin from the ER to the cytosol.","method":"Sequential co-immunoprecipitation; confocal microscopy; genetic screen yielding dominant-negative HEDJ truncation","journal":"Infection and immunity","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP of three-component complex (Stx–HEDJ–Sec61), single lab, supported by dominant-negative truncation phenotype","pmids":["15784599"],"is_preprint":false},{"year":2007,"finding":"XBP-1(S) directly binds the ERdj3 promoter in plasmacytoma cells and LPS-stimulated primary B cells, establishing ERdj3 as a direct transcriptional target of XBP-1(S) during plasma cell differentiation and the UPR.","method":"Chromatin immunoprecipitation (ChIP); shRNA-mediated XBP-1 knockdown; gel shift (EMSA)","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP and EMSA across two cell types (plasmacytoma and primary B cells), with functional confirmation by shRNA knockdown","pmids":["17709512"],"is_preprint":false},{"year":2008,"finding":"Release of ERdj3 from unfolded substrates requires a functional interaction with BiP including both direct physical contact and the ability to stimulate BiP's ATPase activity; BiP mutants defective at any step of the ATPase cycle fail to release ERdj3 from substrate, demonstrating ATP hydrolysis by BiP is mechanistically required for ERdj3 dissociation.","method":"ERdj3 and BiP interaction-disrupting mutants; BiP ATPase cycle mutants; co-immunoprecipitation; in vitro release assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — systematic mutagenesis of both ERdj3 and BiP combined with functional release assays; multiple orthogonal mutant series in a single study","pmids":["18923428"],"is_preprint":false},{"year":2009,"finding":"ERdj3 binds unfolded substrates directly via conserved residues in domain I (homologous to peptide-binding site of yeast Ydj1) and domain II; domain II is critical for substrate binding and is not present in type II DnaJ family members. ERdj3 forms multimers in cells and the conserved C-terminal phenylalanine 326 is critical for self-assembly; mutation of F326A diminishes substrate binding, indicating multimerization is required for full substrate binding activity.","method":"Site-directed mutagenesis of conserved residues; in vitro and in vivo substrate binding assays; secondary structure prediction guided by Ydj1 crystal structure","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — mutagenesis of multiple residues with in vitro and in vivo binding assays; structure-guided design; multiple orthogonal results in one study","pmids":["19090675"],"is_preprint":false},{"year":2010,"finding":"The Salmonella T3SS effector SlrP targets ERdj3 domain II for interaction; SlrP co-localizes partially to the ER and interferes with ERdj3 binding to a denatured substrate, demonstrating SlrP modulates ERdj3 chaperone function in the ER.","method":"Co-immunoprecipitation with truncated ERdj3 constructs; confocal microscopy; subcellular fractionation; substrate binding competition assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — domain mapping with truncations, subcellular localization confirmed by two methods, substrate binding interference assay; single lab","pmids":["20335166"],"is_preprint":false},{"year":2010,"finding":"ERdj3/DNAJB11 is a cellular binding partner and co-chaperone required for expression of the KSHV K1 oncoprotein; siRNA knockdown of ERdj3 dramatically reduces K1 protein levels and abolishes K1's anti-apoptotic function, identifying K1 as an ERdj3 client protein.","method":"Tandem affinity purification; bidirectional co-immunoprecipitation; siRNA knockdown; apoptosis assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP plus functional siRNA knockdown with apoptosis phenotype; single lab","pmids":["20418907"],"is_preprint":false},{"year":2011,"finding":"ERdj3 directly binds unfolded (but not folded) cholera toxin CTA1 subunit via its A1(2) subdomain, masking solvent-exposed hydrophobic residues; expression of dominant-negative ERdj3 blocks CTA1 translocation into the cytosol, establishing ERdj3 as a host factor required for CT intoxication.","method":"Surface plasmon resonance binding assay; dominant-negative ERdj3 overexpression; cell-based translocation assay","journal":"Infection and immunity","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — quantitative SPR binding combined with cell-based functional dominant-negative assay; single lab","pmids":["21844235"],"is_preprint":false},{"year":2013,"finding":"ERdj3 associates with a large complex including the translocon Sec61α in the ER; FRAP analysis shows overexpressed ERdj3 dramatically decreases BiP mobility in a client-dependent manner, while ERdj3 itself remains relatively immobile regardless of client levels, demonstrating ERdj3 regulates BiP engagement of client proteins and likely acts in ER subdomains enriched near the translocon.","method":"FRAP live-cell imaging; native gel electrophoresis; co-immunoprecipitation","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — FRAP combined with native gel and co-IP; single lab but two orthogonal methods","pmids":["23378021"],"is_preprint":false},{"year":2014,"finding":"ERdj3 homodimers that cannot stimulate BiP ATPase (QPD mutants) accumulate on unfolded ER substrates due to impaired release rather than enhanced binding; dimerization is strictly required for substrate binding; heterodimers with one functional subunit show wild-type release rates, demonstrating only one protomer needs to stimulate BiP ATPase for ERdj3 release.","method":"QPD mutant co-expression; pulse-chase experiments; co-immunoprecipitation; heterodimer analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — systematic mutagenesis, pulse-chase kinetics, and heterodimer epistasis all in one study; multiple orthogonal approaches establish mechanism","pmids":["25143379"],"is_preprint":false},{"year":2014,"finding":"ERdj3 promotes ERAD of mutant GCase (Gaucher's disease variants); depleting ERdj3 reduces mutant GCase degradation rate and redirects it to the calnexin pro-folding pathway, increasing GCase trafficking and lysosomal function.","method":"GCase immunoprecipitation followed by mass-spectrometry proteomics; siRNA ERdj3 depletion in patient-derived fibroblasts; GCase trafficking and activity assays","journal":"Chemistry & biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-identified interaction validated by siRNA depletion with quantitative functional readouts; single lab","pmids":["25126989"],"is_preprint":false},{"year":2014,"finding":"UPR activation upregulates and triggers secretion of ERdj3 into the extracellular space; secreted ERdj3 binds misfolded extracellular proteins, substoichiometrically inhibits their aggregation, and attenuates proteotoxicity of misfolded prion protein. ERdj3 can co-secrete with destabilized aggregation-prone clients as a stable complex when ER chaperoning is overwhelmed.","method":"ERdj3 secretion assays under UPR activation; co-secretion co-immunoprecipitation; aggregation inhibition assays; proteotoxicity cell-based assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal functional assays (secretion, co-secretion complex, aggregation inhibition, cell toxicity) across multiple proteins; single lab with comprehensive mechanistic characterization","pmids":["25361606"],"is_preprint":false},{"year":2017,"finding":"ERdj3 promotes ERAD of Z-variant alpha-1-antitrypsin (ZAAT); depleting ERdj3 increases ZAAT degradation rate by redirecting ZAAT to the calreticulin-EDEM1 pathway followed by autophagosome formation.","method":"Co-immunoprecipitation; siRNA ERdj3 knockdown in hepatocytes; degradation rate assays; pathway marker analysis","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP plus functional siRNA depletion with pathway redirection analysis; single lab","pmids":["28419579"],"is_preprint":false},{"year":2017,"finding":"ERdj3/DNAJB11 assembles as a native tetramer (dimer of dimers) rather than the dimer typical of other HSP40 co-chaperones; an EM structural model shows the tetramer involves inter-subunit interactions via domain II and domain III. Deletion of residues 175–190 within domain II renders ERdj3 a stable dimer with impaired substrate binding in the ER and extracellular space, reduced BiP interactions, and worsened ER stress-dependent client secretion and extracellular aggregation.","method":"Electron microscopy structural modeling; targeted domain deletion mutagenesis; co-immunoprecipitation; secretion and aggregation assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — EM structural model combined with mutagenesis, multiple functional assays (substrate binding, BiP interaction, secretion, aggregation); single lab but multiple orthogonal methods","pmids":["28655754"],"is_preprint":false},{"year":2018,"finding":"DNAJB11 loss impairs maturation and trafficking of the ADPKD protein polycystin-1 (PC1) and the ADTKD protein uromodulin (UMOD), establishing DNAJB11 as an ER co-chaperone required for processing of these disease-relevant clients.","method":"Characterization of DNAJB11-null cells; analysis of kidney samples from affected individuals; biochemical trafficking and maturation assays","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — null cell lines plus human tissue; two client proteins examined; single study","pmids":["29706351"],"is_preprint":false},{"year":2019,"finding":"SDF2L1 retains ERdj3 in the ER by forming a complex with ERdj3 and SDF2; the ERdj3 dimer incorporates two SDF2L1 molecules to form the ER-retained complex, whereas ERdj3 alone forms a homotetramer. The ERdj3–SDF2L1 complex shows higher chaperone activity than ERdj3 alone (suppressing ER protein aggregation without requiring substrate transfer to BiP) and maintains denatured GST in a soluble oligomeric state in vitro.","method":"Co-immunoprecipitation; in vitro aggregation suppression assay with denatured GST; intracellular localization analysis; in vitro reconstitution of ERdj3–SDF2L1 complex","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro reconstitution and functional assay combined with in cellulo localization and co-IP; multiple orthogonal methods; single lab","pmids":["31624144"],"is_preprint":false},{"year":2023,"finding":"Dnajb11 loss in mice causes a profound defect in PC1 GPS cleavage with no effect on other cystoprotein processing assayed; conditional Dnajb11 loss in renal tubular epithelium produces PC1 dosage-dependent kidney cysts; Dnajb11 mouse models show no UPR activation or cyst-independent fibrosis, placing DNAJB11-kidney disease on the ADPKD spectrum via a PC1-dependent mechanism distinct from ADTKD pathogenesis.","method":"Germline and conditional mouse knockout alleles; Dnajb11-/- cell lines; PC1 C-terminal fragment cleavage assay; UPR activation markers","journal":"Journal of the American Society of Nephrology","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo mouse models (germline + conditional) combined with cell-line biochemical assays; multiple alleles and readouts; replicated PC1 cleavage defect finding","pmids":["37332102"],"is_preprint":false},{"year":2024,"finding":"ATM kinase phosphorylates DNAJB11 at threonine 188 upon DNA double-strand breaks; this phosphorylation specifically facilitates delivery of misfolded α-synuclein (but not tau or transthyretin) to the HSP70 folding system, and loss of this response impairs neurite outgrowth.","method":"Large-scale proteomic analysis of ATM/ATR substrates; site-directed mutagenesis of T188; co-chaperone delivery assays; neurite outgrowth assay; correlation with transgenic PD mouse model and patient samples","journal":"NAR molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — substrate-specific phosphorylation identified by proteomics and validated by mutagenesis with functional readouts; single lab","pmids":["41256008"],"is_preprint":false},{"year":2024,"finding":"BiP/ERdj3 act as mechanical foldases under force (e.g., during co-translational folding through cellular tunnels), transitioning to holdase function in the absence of force; this force-regulated behavior is opposite to their cytoplasmic homologs DnaK/DnaJ, which act as holdases under force.","method":"Single-molecule force spectroscopy assays; comparison with DnaK/DnaJ homologs","journal":"Protein science","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro single-molecule reconstitution but single study; novel finding not yet replicated","pmids":["38864739"],"is_preprint":false},{"year":2024,"finding":"Biallelic loss of Dnajb11 in mouse models causes cystic kidney disease and fibrosis; cysts originate predominantly from proximal tubules (distinct from classical ADPKD); impaired PC1 GPS cleavage is identified as the underlying molecular mechanism by proteomic analysis of Dnajb11- and Pkd1-deficient cells.","method":"Constitutive and conditional Dnajb11 knockout mouse models; Dnajb11-deficient renal epithelial cell lines; quantitative proteomics; PC1 cleavage assay","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple mouse models combined with proteomics and biochemical PC1 cleavage assay; several orthogonal approaches confirming PC1 mechanism","pmids":["39530576"],"is_preprint":false},{"year":2025,"finding":"SDF2 and SDF2L1 are essential co-factors of DNAJB11 for PC1 processing; unbiased interaction proteomics identifies SDF2/SDF2L1 as strong DNAJB11 interactors; knockout of SDF2 and SDF2L1 together impairs PC1 processing, phenocopying DNAJB11 loss; DNAJB11 and SDF2/SDF2L1 show reciprocal interdependence of protein abundance.","method":"Unbiased interaction proteomics (AP-MS); CRISPR/Cas9 knockout cell lines; PC1 processing assays; complementation re-expression experiments","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — AP-MS interaction discovery validated by multiple knockout cell lines and functional rescue complementation; multiple orthogonal approaches","pmids":["41109348"],"is_preprint":false},{"year":2025,"finding":"The E3 ubiquitin ligase RFFL ubiquitinates DNAJB11 and promotes its degradation via the proteasomal pathway, identifying RFFL as a writer of ubiquitin on DNAJB11.","method":"Label-free quantitative mass spectrometry proteomics; CRISPR/Cas9 RFFL knockout; stable RFFL re-expression; in vivo ubiquitination assays","journal":"Journal of proteome research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proteomics screen validated by multiple complementary cell lines and in vivo ubiquitination assay; single lab","pmids":["40568870"],"is_preprint":false}],"current_model":"DNAJB11 (ERdj3/HEDJ) is a luminal, ER-resident HSP40 co-chaperone that assembles as a tetramer (dimer of dimers involving domain II and III) and functions by directly binding unfolded substrate proteins via domains I and II, stimulating BiP's ATPase activity through its J domain to load clients onto BiP, and then dissociating from substrates in a process that requires ATP hydrolysis by BiP; its ER retention depends on complex formation with SDF2/SDF2L1 (which also enhances chaperone activity), while under ER stress ERdj3 is secreted extracellularly to suppress protein aggregation; it is a direct XBP-1(S) transcriptional target; it facilitates ERAD of misfolded clients including mutant GCase and ZAAT; it is required for correct GPS cleavage and maturation of polycystin-1 (PC1) in a SDF2/SDF2L1-dependent complex, with loss causing PC1-dosage-dependent cyst formation; it undergoes ATM-mediated phosphorylation at T188 to specifically chaperone α-synuclein upon DNA damage; and it is subject to proteasomal degradation mediated by the E3 ligase RFFL."},"narrative":{"mechanistic_narrative":"DNAJB11 (ERdj3/HEDJ) is a luminal, ER-resident HSP40 co-chaperone that orchestrates folding triage in the ER lumen by directly capturing unfolded substrates and handing them to the Hsp70 chaperone BiP [PMID:10827079, PMID:15525676]. Its J domain interacts with BiP in an ATP-dependent manner and stimulates BiP's ATPase activity [PMID:10827079]; substrate binding occurs independently of BiP through conserved residues in domains I and II, with ERdj3 engaging clients first to prevent aggregation and then dissociating before folding completes [PMID:15525676, PMID:19090675]. Substrate release is mechanistically coupled to BiP's catalytic cycle—both physical contact and ATP hydrolysis by BiP are required, and only one protomer of the assembly need stimulate BiP ATPase for release [PMID:18923428, PMID:25143379]. Self-assembly is central to function: ERdj3 forms a native tetramer (dimer of dimers) through inter-subunit contacts in domains II and III, and dimerization is strictly required for substrate binding [PMID:19090675, PMID:28655754]. ER retention and enhanced chaperone activity depend on forming a complex with SDF2/SDF2L1, in which two SDF2L1 molecules incorporate into the ERdj3 dimer and which can hold denatured clients soluble without transfer to BiP [PMID:31624144, PMID:41109348]. DNAJB11 is a direct transcriptional target of XBP-1(S) during the UPR and plasma cell differentiation [PMID:17709512], and under ER stress it is secreted extracellularly where it substoichiometrically suppresses aggregation of misfolded proteins [PMID:25361606]. The chaperone routes specific misfolded clients—including mutant glucocerebrosidase and Z-variant alpha-1-antitrypsin—toward ERAD [PMID:25126989, PMID:28419579]. It is required for maturation and GPS cleavage of polycystin-1 in an SDF2/SDF2L1-dependent manner, and its loss causes PC1-dosage-dependent cystic kidney disease on the ADPKD spectrum [PMID:29706351, PMID:37332102, PMID:41109348]. DNAJB11 additionally acquires a DNA-damage-responsive role through ATM-mediated phosphorylation at T188, which directs misfolded α-synuclein to the HSP70 system [PMID:41256008], and its abundance is controlled by RFFL-mediated ubiquitination and proteasomal degradation [PMID:40568870].","teleology":[{"year":2000,"claim":"Establishing DNAJB11 as a bona fide ER luminal co-chaperone answered where and with which Hsp70 it acts, anchoring all later mechanism.","evidence":"Confocal localization, topology assays, and in vitro ATPase stimulation in a single study","pmids":["10827079"],"confidence":"High","gaps":["Did not define which substrates it binds","Structural basis of BiP interaction not resolved"]},{"year":2004,"claim":"Showing ERdj3 binds unfolded substrates directly and dissociates before folding completes defined its order of action relative to BiP and its anti-aggregation role.","evidence":"In vitro ATPase-dead mutant, co-IP of unfolded clients, and pulse-chase kinetics","pmids":["15525676","15544163"],"confidence":"High","gaps":["Substrate-binding residues not yet mapped","Mechanism of release not biochemically dissected"]},{"year":2007,"claim":"Identifying DNAJB11 as a direct XBP-1(S) target placed it within the UPR transcriptional program and secretory-cell biology.","evidence":"ChIP and EMSA in plasmacytoma and primary B cells with shRNA XBP-1 knockdown","pmids":["17709512"],"confidence":"High","gaps":["Other UPR arms' contribution to induction not addressed"]},{"year":2009,"claim":"Mapping substrate-binding to domains I and II and showing F326-dependent multimerization explained how the chaperone recognizes clients and that self-assembly enables full activity.","evidence":"Structure-guided mutagenesis with in vitro and in vivo binding assays","pmids":["19090675"],"confidence":"High","gaps":["Exact oligomeric architecture not resolved at this stage"]},{"year":2008,"claim":"Demonstrating that BiP ATP hydrolysis is required to release ERdj3 from substrate closed the loop on the handoff mechanism.","evidence":"BiP ATPase-cycle mutants and ERdj3 interaction mutants with in vitro release assays","pmids":["18923428"],"confidence":"High","gaps":["Did not address stoichiometry of release per oligomer"]},{"year":2014,"claim":"Resolving that dimerization is required for binding while only one protomer must stimulate BiP for release refined the catalytic logic of the chaperone cycle.","evidence":"QPD mutant and heterodimer epistasis with pulse-chase kinetics","pmids":["25143379"],"confidence":"High","gaps":["Higher-order tetramer not yet recognized in this work"]},{"year":2014,"claim":"Showing UPR-triggered secretion of ERdj3 extended its anti-aggregation function beyond the ER into the extracellular space.","evidence":"Secretion and co-secretion assays, aggregation inhibition, and proteotoxicity cell assays","pmids":["25361606"],"confidence":"High","gaps":["Physiological extracellular substrates in vivo not defined","Regulation of the secretory decision unclear"]},{"year":2014,"claim":"Identifying DNAJB11 as a determinant of ERAD routing for disease-variant clients (mutant GCase, ZAAT) linked the chaperone to degradative triage decisions.","evidence":"IP-MS interaction, siRNA depletion, and pathway-redirection/degradation assays in patient-derived cells","pmids":["25126989","28419579"],"confidence":"Medium","gaps":["Direct vs indirect ERAD targeting not fully separated","Single-lab characterization per client"]},{"year":2017,"claim":"Discovering the native tetramer (dimer of dimers) via domains II/III redefined the functional unit beyond canonical HSP40 dimers.","evidence":"EM structural modeling with domain-deletion mutagenesis and functional assays","pmids":["28655754"],"confidence":"High","gaps":["High-resolution structure not obtained","Dynamics of oligomer interconversion unclear"]},{"year":2018,"claim":"Linking DNAJB11 loss to defective maturation of polycystin-1 and uromodulin connected its chaperone activity to human kidney disease clients.","evidence":"DNAJB11-null cells and affected human kidney tissue with trafficking/maturation assays","pmids":["29706351"],"confidence":"Medium","gaps":["Causal in vivo mechanism not yet established","Whether PC1 or UMOD defect drives disease unresolved"]},{"year":2019,"claim":"Defining the ERdj3–SDF2/SDF2L1 complex explained ER retention and an enhanced, BiP-independent chaperone mode.","evidence":"In vitro reconstitution, aggregation suppression with denatured GST, co-IP, and localization analysis","pmids":["31624144"],"confidence":"High","gaps":["Structural detail of the complex not resolved","Switch between tetramer and SDF2L1-bound state not defined"]},{"year":2023,"claim":"Mouse models established that DNAJB11 kidney disease arises from a PC1-specific GPS cleavage defect on the ADPKD spectrum, distinct from ADTKD/UPR mechanisms.","evidence":"Germline and conditional knockout mice, null cell lines, PC1 cleavage and UPR-marker assays","pmids":["37332102","39530576"],"confidence":"High","gaps":["Molecular step of GPS cleavage facilitation not defined","Why PC1 is uniquely sensitive unclear"]},{"year":2024,"claim":"Identifying ATM phosphorylation of T188 revealed a DNA-damage-responsive, substrate-specific chaperone function for α-synuclein delivery to HSP70.","evidence":"Phosphoproteomics, T188 mutagenesis, co-chaperone delivery and neurite outgrowth assays","pmids":["41256008"],"confidence":"Medium","gaps":["How an ER co-chaperone accesses cytoplasmic ATM signaling unclear","Single-lab finding"]},{"year":2025,"claim":"Validating SDF2/SDF2L1 as essential PC1-processing cofactors and RFFL as the degradative ligase tied the chaperone complex and its turnover to disease-relevant client processing.","evidence":"AP-MS, CRISPR knockouts with PC1 processing/rescue, label-free MS, and in vivo ubiquitination assays","pmids":["41109348","40568870"],"confidence":"High","gaps":["RFFL regulation of DNAJB11 in physiological/disease contexts not established","Whether SDF2/SDF2L1 directly contact PC1 unknown"]},{"year":null,"claim":"How DNAJB11 mechanistically facilitates the specific GPS autoproteolytic cleavage of polycystin-1, and how this is integrated with its tetramer/SDF2L1 states, remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of DNAJB11 with PC1 or SDF2L1","Molecular basis of PC1 client selectivity unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[0,1,6,13,17]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,5,11]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,5,10]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,10,17]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[13]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,5,11]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[2,4,13]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[12,14,16,18,21]}],"complexes":["ERdj3–SDF2–SDF2L1 complex","ERdj3 homotetramer (dimer of dimers)"],"partners":["HSPA5","SDF2L1","SDF2","SEC61A1","RFFL"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UBS4","full_name":"DnaJ homolog subfamily B member 11","aliases":["APOBEC1-binding protein 2","ABBP-2","DnaJ protein homolog 9","ER-associated DNAJ","ER-associated Hsp40 co-chaperone","Endoplasmic reticulum DNA J domain-containing protein 3","ER-resident protein ERdj3","ERdj3","ERj3p","HEDJ","Human DnaJ protein 9","hDj-9","PWP1-interacting protein 4"],"length_aa":358,"mass_kda":40.5,"function":"As a co-chaperone for HSPA5 it is required for proper folding, trafficking or degradation of proteins (PubMed:10827079, PubMed:15525676, PubMed:29706351). Binds directly to both unfolded proteins that are substrates for ERAD and nascent unfolded peptide chains, but dissociates from the HSPA5-unfolded protein complex before folding is completed (PubMed:15525676). May help recruiting HSPA5 and other chaperones to the substrate. Stimulates HSPA5 ATPase activity (PubMed:10827079). It is necessary for maturation and correct trafficking of PKD1 (PubMed:29706351)","subcellular_location":"Endoplasmic reticulum lumen","url":"https://www.uniprot.org/uniprotkb/Q9UBS4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNAJB11","classification":"Not Classified","n_dependent_lines":150,"n_total_lines":1208,"dependency_fraction":0.12417218543046357},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CANX","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"SNX1","stoichiometry":0.2},{"gene":"SNX2","stoichiometry":0.2},{"gene":"SNX5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/DNAJB11","total_profiled":1310},"omim":[{"mim_id":"618061","title":"POLYCYSTIC KIDNEY DISEASE 6 WITH OR WITHOUT POLYCYSTIC LIVER DISEASE; PKD6","url":"https://www.omim.org/entry/618061"},{"mim_id":"617435","title":"LOPES-MACIEL-RODAN SYNDROME; LOMARS","url":"https://www.omim.org/entry/617435"},{"mim_id":"613004","title":"HUNTINGTIN; HTT","url":"https://www.omim.org/entry/613004"},{"mim_id":"611341","title":"DNAJ/HSP40 HOMOLOG, SUBFAMILY B, MEMBER 11; DNAJB11","url":"https://www.omim.org/entry/611341"},{"mim_id":"173900","title":"POLYCYSTIC KIDNEY DISEASE 1 WITH OR WITHOUT POLYCYSTIC LIVER DISEASE; PKD1","url":"https://www.omim.org/entry/173900"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Endoplasmic reticulum","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DNAJB11"},"hgnc":{"alias_symbol":["EDJ","HEDJ","ERdj3"],"prev_symbol":[]},"alphafold":{"accession":"Q9UBS4","domains":[{"cath_id":"1.10.287.110","chopping":"23-92","consensus_level":"medium","plddt":86.113,"start":23,"end":92},{"cath_id":"2.60.260.20","chopping":"133-244","consensus_level":"high","plddt":91.6085,"start":133,"end":244},{"cath_id":"2.60.260.20","chopping":"250-342","consensus_level":"high","plddt":94.4131,"start":250,"end":342}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBS4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBS4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBS4-F1-predicted_aligned_error_v6.png","plddt_mean":84.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNAJB11","jax_strain_url":"https://www.jax.org/strain/search?query=DNAJB11"},"sequence":{"accession":"Q9UBS4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UBS4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UBS4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBS4"}},"corpus_meta":[{"pmid":"29706351","id":"PMC_29706351","title":"Monoallelic Mutations to DNAJB11 Cause Atypical Autosomal-Dominant Polycystic Kidney Disease.","date":"2018","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29706351","citation_count":237,"is_preprint":false},{"pmid":"15525676","id":"PMC_15525676","title":"ERdj3, a stress-inducible endoplasmic reticulum DnaJ homologue, serves as a cofactor for BiP's interactions with unfolded substrates.","date":"2004","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/15525676","citation_count":166,"is_preprint":false},{"pmid":"25361606","id":"PMC_25361606","title":"Unfolded protein response-induced ERdj3 secretion links ER stress to extracellular proteostasis.","date":"2014","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/25361606","citation_count":105,"is_preprint":false},{"pmid":"10827079","id":"PMC_10827079","title":"HEDJ, an Hsp40 co-chaperone localized to the endoplasmic reticulum of human cells.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10827079","citation_count":94,"is_preprint":false},{"pmid":"15784599","id":"PMC_15784599","title":"Shiga toxin is transported from the endoplasmic reticulum following interaction with the luminal chaperone HEDJ/ERdj3.","date":"2005","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/15784599","citation_count":93,"is_preprint":false},{"pmid":"18923428","id":"PMC_18923428","title":"Regulated release of ERdj3 from unfolded proteins by BiP.","date":"2008","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/18923428","citation_count":68,"is_preprint":false},{"pmid":"20335166","id":"PMC_20335166","title":"The Salmonella type III secretion effector, salmonella leucine-rich repeat protein (SlrP), targets the human chaperone ERdj3.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20335166","citation_count":67,"is_preprint":false},{"pmid":"19090675","id":"PMC_19090675","title":"ERdj3, a luminal ER DnaJ homologue, binds directly to unfolded proteins in the mammalian ER: identification of critical residues.","date":"2009","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19090675","citation_count":63,"is_preprint":false},{"pmid":"25126989","id":"PMC_25126989","title":"ERdj3 is an endoplasmic reticulum degradation factor for mutant glucocerebrosidase variants linked to Gaucher's disease.","date":"2014","source":"Chemistry & biology","url":"https://pubmed.ncbi.nlm.nih.gov/25126989","citation_count":62,"is_preprint":false},{"pmid":"20418907","id":"PMC_20418907","title":"Hsp90 and Hsp40/Erdj3 are required for the expression and anti-apoptotic function of KSHV K1.","date":"2010","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/20418907","citation_count":55,"is_preprint":false},{"pmid":"23378021","id":"PMC_23378021","title":"ERdj3 regulates BiP occupancy in living cells.","date":"2013","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/23378021","citation_count":44,"is_preprint":false},{"pmid":"28655754","id":"PMC_28655754","title":"The endoplasmic reticulum HSP40 co-chaperone ERdj3/DNAJB11 assembles and functions as a tetramer.","date":"2017","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/28655754","citation_count":43,"is_preprint":false},{"pmid":"31624144","id":"PMC_31624144","title":"SDF2-like protein 1 (SDF2L1) regulates the endoplasmic reticulum localization and chaperone activity of ERdj3 protein.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31624144","citation_count":28,"is_preprint":false},{"pmid":"17709512","id":"PMC_17709512","title":"Identification of ERdj3 and OBF-1/BOB-1/OCA-B as direct targets of XBP-1 during plasma cell differentiation.","date":"2007","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/17709512","citation_count":26,"is_preprint":false},{"pmid":"36209075","id":"PMC_36209075","title":"Exosomal DNAJB11 promotes the development of pancreatic cancer by modulating the EGFR/MAPK pathway.","date":"2022","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/36209075","citation_count":21,"is_preprint":false},{"pmid":"15544163","id":"PMC_15544163","title":"Localization and function in endoplasmic reticulum stress tolerance of ERdj3, a new member of Hsp40 family protein.","date":"2004","source":"Cell stress & chaperones","url":"https://pubmed.ncbi.nlm.nih.gov/15544163","citation_count":21,"is_preprint":false},{"pmid":"28419579","id":"PMC_28419579","title":"Erdj3 Has an Essential Role for Z Variant Alpha-1-Antitrypsin Degradation.","date":"2017","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28419579","citation_count":21,"is_preprint":false},{"pmid":"21844235","id":"PMC_21844235","title":"Structural and functional interactions between the cholera toxin A1 subunit and ERdj3/HEDJ, a chaperone of the endoplasmic reticulum.","date":"2011","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/21844235","citation_count":19,"is_preprint":false},{"pmid":"25143379","id":"PMC_25143379","title":"Dissection of structural and functional requirements that underlie the interaction of ERdj3 protein with substrates in the endoplasmic reticulum.","date":"2014","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/25143379","citation_count":17,"is_preprint":false},{"pmid":"33129895","id":"PMC_33129895","title":"Bi-allelic pathogenic variations in DNAJB11 cause Ivemark II syndrome, a renal-hepatic-pancreatic dysplasia.","date":"2020","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/33129895","citation_count":17,"is_preprint":false},{"pmid":"29992839","id":"PMC_29992839","title":"The endoplasmic reticulum co-chaperone ERdj3/DNAJB11 promotes hepatocellular carcinoma progression through suppressing AATZ degradation.","date":"2018","source":"Future oncology (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/29992839","citation_count":13,"is_preprint":false},{"pmid":"35664268","id":"PMC_35664268","title":"More dissimilarities than affinities between DNAJB11-PKD and ADPKD.","date":"2022","source":"Clinical kidney journal","url":"https://pubmed.ncbi.nlm.nih.gov/35664268","citation_count":12,"is_preprint":false},{"pmid":"37332102","id":"PMC_37332102","title":"Dnajb11-Kidney Disease Develops from Reduced Polycystin-1 Dosage but not Unfolded Protein Response in Mice.","date":"2023","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/37332102","citation_count":7,"is_preprint":false},{"pmid":"39530576","id":"PMC_39530576","title":"The role of the co-chaperone DNAJB11 in polycystic kidney disease: Molecular mechanisms and cellular origin of cyst formation.","date":"2024","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/39530576","citation_count":5,"is_preprint":false},{"pmid":"38864739","id":"PMC_38864739","title":"Force-regulated chaperone activity of BiP/ERdj3 is opposite to their homologs DnaK/DnaJ.","date":"2024","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/38864739","citation_count":5,"is_preprint":false},{"pmid":"41256008","id":"PMC_41256008","title":"ATM-mediated co-chaperone DNAJB11 phosphorylation facilitates α-synuclein folding upon DNA double-stranded breaks.","date":"2024","source":"NAR molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41256008","citation_count":4,"is_preprint":false},{"pmid":"38275584","id":"PMC_38275584","title":"DNAJB11 Mutation in ADPKD Patients: Clinical Characteristics in a Monocentric Cohort.","date":"2023","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/38275584","citation_count":3,"is_preprint":false},{"pmid":"40568870","id":"PMC_40568870","title":"Quantitative Proteomic Analysis Reveals JMJD6 and DNAJB11 as Endogenous Substrates of E3 Ligase RFFL.","date":"2025","source":"Journal of proteome research","url":"https://pubmed.ncbi.nlm.nih.gov/40568870","citation_count":1,"is_preprint":false},{"pmid":"28752709","id":"PMC_28752709","title":"[Expression and clinical significance of DNAJB11 in epithelial ovarian cancer].","date":"2017","source":"Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/28752709","citation_count":1,"is_preprint":false},{"pmid":"37867501","id":"PMC_37867501","title":"Atypical ADPKD Due to a DNAJB11 Pathogenic Variant: An Educational Case Report.","date":"2023","source":"Canadian journal of kidney health and disease","url":"https://pubmed.ncbi.nlm.nih.gov/37867501","citation_count":1,"is_preprint":false},{"pmid":"41109348","id":"PMC_41109348","title":"SDF2 and SDF2L1 are essential co-factors of DNAJB11 for Polycystin-1 processing.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41109348","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17335,"output_tokens":6116,"usd":0.071873,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":14841,"output_tokens":4177,"usd":0.089315,"stage2_stop_reason":"end_turn"},"total_usd":0.161188,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"HEDJ/DNAJB11 is a luminal, membrane-associated ER-resident Hsp40 co-chaperone whose J domain interacts with the ER-associated Hsp70 BiP in an ATP-dependent manner and stimulates BiP's ATPase activity in vitro.\",\n      \"method\": \"Confocal microscopy for ER localization; protease susceptibility, glycosidase treatment, detergent solubility assays for luminal orientation; in vitro ATPase stimulation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal biochemical methods (localization, topology, in vitro ATPase assay) in a single study; replicated by subsequent work\",\n      \"pmids\": [\"10827079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"ERdj3 directly binds unfolded protein substrates (unassembled Ig heavy chains, unfolded light chains, VSV-G ts045 mutant) independently of BiP; an ERdj3 mutant unable to stimulate BiP's ATPase activity in vitro or bind BiP in vivo retains substrate binding, indicating ERdj3 contacts substrates directly rather than via BiP. ERdj3 binds substrates first and dissociates before folding is complete, whereas BiP remains bound longer, supporting a model where ERdj3 inhibits aggregation until BiP joins and then BiP-interaction triggers ERdj3 release.\",\n      \"method\": \"In vitro ATPase stimulation assay; co-immunoprecipitation; ERdj3 ATPase-stimulation-dead mutant; pulse-chase kinetics\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro mutagenesis combined with in vivo co-IP; mechanistic model supported by multiple orthogonal experiments; replicated in subsequent studies\",\n      \"pmids\": [\"15525676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"ERdj3 is moderately induced by ER stressors; siRNA-mediated reduction of ERdj3 decreases ER stress tolerance in neuroblastoma cells, while overexpression of ERdj3 suppresses vero toxin-induced cell death.\",\n      \"method\": \"siRNA knockdown; ERdj3 overexpression by gene transfection; cell viability assays\",\n      \"journal\": \"Cell stress & chaperones\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — clean KD/KO with defined phenotypic readout, single lab\",\n      \"pmids\": [\"15544163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Within the ER lumen, Shiga toxin interacts with HEDJ/ERdj3 and is found in a complex containing HEDJ and the translocon Sec61, suggesting ERdj3 participates in retrotranslocation of Shiga toxin from the ER to the cytosol.\",\n      \"method\": \"Sequential co-immunoprecipitation; confocal microscopy; genetic screen yielding dominant-negative HEDJ truncation\",\n      \"journal\": \"Infection and immunity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP of three-component complex (Stx–HEDJ–Sec61), single lab, supported by dominant-negative truncation phenotype\",\n      \"pmids\": [\"15784599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"XBP-1(S) directly binds the ERdj3 promoter in plasmacytoma cells and LPS-stimulated primary B cells, establishing ERdj3 as a direct transcriptional target of XBP-1(S) during plasma cell differentiation and the UPR.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP); shRNA-mediated XBP-1 knockdown; gel shift (EMSA)\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP and EMSA across two cell types (plasmacytoma and primary B cells), with functional confirmation by shRNA knockdown\",\n      \"pmids\": [\"17709512\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Release of ERdj3 from unfolded substrates requires a functional interaction with BiP including both direct physical contact and the ability to stimulate BiP's ATPase activity; BiP mutants defective at any step of the ATPase cycle fail to release ERdj3 from substrate, demonstrating ATP hydrolysis by BiP is mechanistically required for ERdj3 dissociation.\",\n      \"method\": \"ERdj3 and BiP interaction-disrupting mutants; BiP ATPase cycle mutants; co-immunoprecipitation; in vitro release assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — systematic mutagenesis of both ERdj3 and BiP combined with functional release assays; multiple orthogonal mutant series in a single study\",\n      \"pmids\": [\"18923428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"ERdj3 binds unfolded substrates directly via conserved residues in domain I (homologous to peptide-binding site of yeast Ydj1) and domain II; domain II is critical for substrate binding and is not present in type II DnaJ family members. ERdj3 forms multimers in cells and the conserved C-terminal phenylalanine 326 is critical for self-assembly; mutation of F326A diminishes substrate binding, indicating multimerization is required for full substrate binding activity.\",\n      \"method\": \"Site-directed mutagenesis of conserved residues; in vitro and in vivo substrate binding assays; secondary structure prediction guided by Ydj1 crystal structure\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — mutagenesis of multiple residues with in vitro and in vivo binding assays; structure-guided design; multiple orthogonal results in one study\",\n      \"pmids\": [\"19090675\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The Salmonella T3SS effector SlrP targets ERdj3 domain II for interaction; SlrP co-localizes partially to the ER and interferes with ERdj3 binding to a denatured substrate, demonstrating SlrP modulates ERdj3 chaperone function in the ER.\",\n      \"method\": \"Co-immunoprecipitation with truncated ERdj3 constructs; confocal microscopy; subcellular fractionation; substrate binding competition assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — domain mapping with truncations, subcellular localization confirmed by two methods, substrate binding interference assay; single lab\",\n      \"pmids\": [\"20335166\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"ERdj3/DNAJB11 is a cellular binding partner and co-chaperone required for expression of the KSHV K1 oncoprotein; siRNA knockdown of ERdj3 dramatically reduces K1 protein levels and abolishes K1's anti-apoptotic function, identifying K1 as an ERdj3 client protein.\",\n      \"method\": \"Tandem affinity purification; bidirectional co-immunoprecipitation; siRNA knockdown; apoptosis assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP plus functional siRNA knockdown with apoptosis phenotype; single lab\",\n      \"pmids\": [\"20418907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"ERdj3 directly binds unfolded (but not folded) cholera toxin CTA1 subunit via its A1(2) subdomain, masking solvent-exposed hydrophobic residues; expression of dominant-negative ERdj3 blocks CTA1 translocation into the cytosol, establishing ERdj3 as a host factor required for CT intoxication.\",\n      \"method\": \"Surface plasmon resonance binding assay; dominant-negative ERdj3 overexpression; cell-based translocation assay\",\n      \"journal\": \"Infection and immunity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — quantitative SPR binding combined with cell-based functional dominant-negative assay; single lab\",\n      \"pmids\": [\"21844235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ERdj3 associates with a large complex including the translocon Sec61α in the ER; FRAP analysis shows overexpressed ERdj3 dramatically decreases BiP mobility in a client-dependent manner, while ERdj3 itself remains relatively immobile regardless of client levels, demonstrating ERdj3 regulates BiP engagement of client proteins and likely acts in ER subdomains enriched near the translocon.\",\n      \"method\": \"FRAP live-cell imaging; native gel electrophoresis; co-immunoprecipitation\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — FRAP combined with native gel and co-IP; single lab but two orthogonal methods\",\n      \"pmids\": [\"23378021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ERdj3 homodimers that cannot stimulate BiP ATPase (QPD mutants) accumulate on unfolded ER substrates due to impaired release rather than enhanced binding; dimerization is strictly required for substrate binding; heterodimers with one functional subunit show wild-type release rates, demonstrating only one protomer needs to stimulate BiP ATPase for ERdj3 release.\",\n      \"method\": \"QPD mutant co-expression; pulse-chase experiments; co-immunoprecipitation; heterodimer analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — systematic mutagenesis, pulse-chase kinetics, and heterodimer epistasis all in one study; multiple orthogonal approaches establish mechanism\",\n      \"pmids\": [\"25143379\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ERdj3 promotes ERAD of mutant GCase (Gaucher's disease variants); depleting ERdj3 reduces mutant GCase degradation rate and redirects it to the calnexin pro-folding pathway, increasing GCase trafficking and lysosomal function.\",\n      \"method\": \"GCase immunoprecipitation followed by mass-spectrometry proteomics; siRNA ERdj3 depletion in patient-derived fibroblasts; GCase trafficking and activity assays\",\n      \"journal\": \"Chemistry & biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-identified interaction validated by siRNA depletion with quantitative functional readouts; single lab\",\n      \"pmids\": [\"25126989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"UPR activation upregulates and triggers secretion of ERdj3 into the extracellular space; secreted ERdj3 binds misfolded extracellular proteins, substoichiometrically inhibits their aggregation, and attenuates proteotoxicity of misfolded prion protein. ERdj3 can co-secrete with destabilized aggregation-prone clients as a stable complex when ER chaperoning is overwhelmed.\",\n      \"method\": \"ERdj3 secretion assays under UPR activation; co-secretion co-immunoprecipitation; aggregation inhibition assays; proteotoxicity cell-based assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal functional assays (secretion, co-secretion complex, aggregation inhibition, cell toxicity) across multiple proteins; single lab with comprehensive mechanistic characterization\",\n      \"pmids\": [\"25361606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ERdj3 promotes ERAD of Z-variant alpha-1-antitrypsin (ZAAT); depleting ERdj3 increases ZAAT degradation rate by redirecting ZAAT to the calreticulin-EDEM1 pathway followed by autophagosome formation.\",\n      \"method\": \"Co-immunoprecipitation; siRNA ERdj3 knockdown in hepatocytes; degradation rate assays; pathway marker analysis\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP plus functional siRNA depletion with pathway redirection analysis; single lab\",\n      \"pmids\": [\"28419579\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ERdj3/DNAJB11 assembles as a native tetramer (dimer of dimers) rather than the dimer typical of other HSP40 co-chaperones; an EM structural model shows the tetramer involves inter-subunit interactions via domain II and domain III. Deletion of residues 175–190 within domain II renders ERdj3 a stable dimer with impaired substrate binding in the ER and extracellular space, reduced BiP interactions, and worsened ER stress-dependent client secretion and extracellular aggregation.\",\n      \"method\": \"Electron microscopy structural modeling; targeted domain deletion mutagenesis; co-immunoprecipitation; secretion and aggregation assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — EM structural model combined with mutagenesis, multiple functional assays (substrate binding, BiP interaction, secretion, aggregation); single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28655754\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DNAJB11 loss impairs maturation and trafficking of the ADPKD protein polycystin-1 (PC1) and the ADTKD protein uromodulin (UMOD), establishing DNAJB11 as an ER co-chaperone required for processing of these disease-relevant clients.\",\n      \"method\": \"Characterization of DNAJB11-null cells; analysis of kidney samples from affected individuals; biochemical trafficking and maturation assays\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — null cell lines plus human tissue; two client proteins examined; single study\",\n      \"pmids\": [\"29706351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SDF2L1 retains ERdj3 in the ER by forming a complex with ERdj3 and SDF2; the ERdj3 dimer incorporates two SDF2L1 molecules to form the ER-retained complex, whereas ERdj3 alone forms a homotetramer. The ERdj3–SDF2L1 complex shows higher chaperone activity than ERdj3 alone (suppressing ER protein aggregation without requiring substrate transfer to BiP) and maintains denatured GST in a soluble oligomeric state in vitro.\",\n      \"method\": \"Co-immunoprecipitation; in vitro aggregation suppression assay with denatured GST; intracellular localization analysis; in vitro reconstitution of ERdj3–SDF2L1 complex\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro reconstitution and functional assay combined with in cellulo localization and co-IP; multiple orthogonal methods; single lab\",\n      \"pmids\": [\"31624144\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Dnajb11 loss in mice causes a profound defect in PC1 GPS cleavage with no effect on other cystoprotein processing assayed; conditional Dnajb11 loss in renal tubular epithelium produces PC1 dosage-dependent kidney cysts; Dnajb11 mouse models show no UPR activation or cyst-independent fibrosis, placing DNAJB11-kidney disease on the ADPKD spectrum via a PC1-dependent mechanism distinct from ADTKD pathogenesis.\",\n      \"method\": \"Germline and conditional mouse knockout alleles; Dnajb11-/- cell lines; PC1 C-terminal fragment cleavage assay; UPR activation markers\",\n      \"journal\": \"Journal of the American Society of Nephrology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo mouse models (germline + conditional) combined with cell-line biochemical assays; multiple alleles and readouts; replicated PC1 cleavage defect finding\",\n      \"pmids\": [\"37332102\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ATM kinase phosphorylates DNAJB11 at threonine 188 upon DNA double-strand breaks; this phosphorylation specifically facilitates delivery of misfolded α-synuclein (but not tau or transthyretin) to the HSP70 folding system, and loss of this response impairs neurite outgrowth.\",\n      \"method\": \"Large-scale proteomic analysis of ATM/ATR substrates; site-directed mutagenesis of T188; co-chaperone delivery assays; neurite outgrowth assay; correlation with transgenic PD mouse model and patient samples\",\n      \"journal\": \"NAR molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — substrate-specific phosphorylation identified by proteomics and validated by mutagenesis with functional readouts; single lab\",\n      \"pmids\": [\"41256008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"BiP/ERdj3 act as mechanical foldases under force (e.g., during co-translational folding through cellular tunnels), transitioning to holdase function in the absence of force; this force-regulated behavior is opposite to their cytoplasmic homologs DnaK/DnaJ, which act as holdases under force.\",\n      \"method\": \"Single-molecule force spectroscopy assays; comparison with DnaK/DnaJ homologs\",\n      \"journal\": \"Protein science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro single-molecule reconstitution but single study; novel finding not yet replicated\",\n      \"pmids\": [\"38864739\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Biallelic loss of Dnajb11 in mouse models causes cystic kidney disease and fibrosis; cysts originate predominantly from proximal tubules (distinct from classical ADPKD); impaired PC1 GPS cleavage is identified as the underlying molecular mechanism by proteomic analysis of Dnajb11- and Pkd1-deficient cells.\",\n      \"method\": \"Constitutive and conditional Dnajb11 knockout mouse models; Dnajb11-deficient renal epithelial cell lines; quantitative proteomics; PC1 cleavage assay\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple mouse models combined with proteomics and biochemical PC1 cleavage assay; several orthogonal approaches confirming PC1 mechanism\",\n      \"pmids\": [\"39530576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SDF2 and SDF2L1 are essential co-factors of DNAJB11 for PC1 processing; unbiased interaction proteomics identifies SDF2/SDF2L1 as strong DNAJB11 interactors; knockout of SDF2 and SDF2L1 together impairs PC1 processing, phenocopying DNAJB11 loss; DNAJB11 and SDF2/SDF2L1 show reciprocal interdependence of protein abundance.\",\n      \"method\": \"Unbiased interaction proteomics (AP-MS); CRISPR/Cas9 knockout cell lines; PC1 processing assays; complementation re-expression experiments\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — AP-MS interaction discovery validated by multiple knockout cell lines and functional rescue complementation; multiple orthogonal approaches\",\n      \"pmids\": [\"41109348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The E3 ubiquitin ligase RFFL ubiquitinates DNAJB11 and promotes its degradation via the proteasomal pathway, identifying RFFL as a writer of ubiquitin on DNAJB11.\",\n      \"method\": \"Label-free quantitative mass spectrometry proteomics; CRISPR/Cas9 RFFL knockout; stable RFFL re-expression; in vivo ubiquitination assays\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proteomics screen validated by multiple complementary cell lines and in vivo ubiquitination assay; single lab\",\n      \"pmids\": [\"40568870\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DNAJB11 (ERdj3/HEDJ) is a luminal, ER-resident HSP40 co-chaperone that assembles as a tetramer (dimer of dimers involving domain II and III) and functions by directly binding unfolded substrate proteins via domains I and II, stimulating BiP's ATPase activity through its J domain to load clients onto BiP, and then dissociating from substrates in a process that requires ATP hydrolysis by BiP; its ER retention depends on complex formation with SDF2/SDF2L1 (which also enhances chaperone activity), while under ER stress ERdj3 is secreted extracellularly to suppress protein aggregation; it is a direct XBP-1(S) transcriptional target; it facilitates ERAD of misfolded clients including mutant GCase and ZAAT; it is required for correct GPS cleavage and maturation of polycystin-1 (PC1) in a SDF2/SDF2L1-dependent complex, with loss causing PC1-dosage-dependent cyst formation; it undergoes ATM-mediated phosphorylation at T188 to specifically chaperone α-synuclein upon DNA damage; and it is subject to proteasomal degradation mediated by the E3 ligase RFFL.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNAJB11 (ERdj3/HEDJ) is a luminal, ER-resident HSP40 co-chaperone that orchestrates folding triage in the ER lumen by directly capturing unfolded substrates and handing them to the Hsp70 chaperone BiP [#0, #1]. Its J domain interacts with BiP in an ATP-dependent manner and stimulates BiP's ATPase activity [#0]; substrate binding occurs independently of BiP through conserved residues in domains I and II, with ERdj3 engaging clients first to prevent aggregation and then dissociating before folding completes [#1, #6]. Substrate release is mechanistically coupled to BiP's catalytic cycle—both physical contact and ATP hydrolysis by BiP are required, and only one protomer of the assembly need stimulate BiP ATPase for release [#5, #11]. Self-assembly is central to function: ERdj3 forms a native tetramer (dimer of dimers) through inter-subunit contacts in domains II and III, and dimerization is strictly required for substrate binding [#6, #15]. ER retention and enhanced chaperone activity depend on forming a complex with SDF2/SDF2L1, in which two SDF2L1 molecules incorporate into the ERdj3 dimer and which can hold denatured clients soluble without transfer to BiP [#17, #22]. DNAJB11 is a direct transcriptional target of XBP-1(S) during the UPR and plasma cell differentiation [#4], and under ER stress it is secreted extracellularly where it substoichiometrically suppresses aggregation of misfolded proteins [#13]. The chaperone routes specific misfolded clients—including mutant glucocerebrosidase and Z-variant alpha-1-antitrypsin—toward ERAD [#12, #14]. It is required for maturation and GPS cleavage of polycystin-1 in an SDF2/SDF2L1-dependent manner, and its loss causes PC1-dosage-dependent cystic kidney disease on the ADPKD spectrum [#16, #18, #22]. DNAJB11 additionally acquires a DNA-damage-responsive role through ATM-mediated phosphorylation at T188, which directs misfolded \\u03b1-synuclein to the HSP70 system [#19], and its abundance is controlled by RFFL-mediated ubiquitination and proteasomal degradation [#23].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Establishing DNAJB11 as a bona fide ER luminal co-chaperone answered where and with which Hsp70 it acts, anchoring all later mechanism.\",\n      \"evidence\": \"Confocal localization, topology assays, and in vitro ATPase stimulation in a single study\",\n      \"pmids\": [\"10827079\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which substrates it binds\", \"Structural basis of BiP interaction not resolved\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showing ERdj3 binds unfolded substrates directly and dissociates before folding completes defined its order of action relative to BiP and its anti-aggregation role.\",\n      \"evidence\": \"In vitro ATPase-dead mutant, co-IP of unfolded clients, and pulse-chase kinetics\",\n      \"pmids\": [\"15525676\", \"15544163\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate-binding residues not yet mapped\", \"Mechanism of release not biochemically dissected\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identifying DNAJB11 as a direct XBP-1(S) target placed it within the UPR transcriptional program and secretory-cell biology.\",\n      \"evidence\": \"ChIP and EMSA in plasmacytoma and primary B cells with shRNA XBP-1 knockdown\",\n      \"pmids\": [\"17709512\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Other UPR arms' contribution to induction not addressed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Mapping substrate-binding to domains I and II and showing F326-dependent multimerization explained how the chaperone recognizes clients and that self-assembly enables full activity.\",\n      \"evidence\": \"Structure-guided mutagenesis with in vitro and in vivo binding assays\",\n      \"pmids\": [\"19090675\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Exact oligomeric architecture not resolved at this stage\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrating that BiP ATP hydrolysis is required to release ERdj3 from substrate closed the loop on the handoff mechanism.\",\n      \"evidence\": \"BiP ATPase-cycle mutants and ERdj3 interaction mutants with in vitro release assays\",\n      \"pmids\": [\"18923428\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address stoichiometry of release per oligomer\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolving that dimerization is required for binding while only one protomer must stimulate BiP for release refined the catalytic logic of the chaperone cycle.\",\n      \"evidence\": \"QPD mutant and heterodimer epistasis with pulse-chase kinetics\",\n      \"pmids\": [\"25143379\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Higher-order tetramer not yet recognized in this work\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showing UPR-triggered secretion of ERdj3 extended its anti-aggregation function beyond the ER into the extracellular space.\",\n      \"evidence\": \"Secretion and co-secretion assays, aggregation inhibition, and proteotoxicity cell assays\",\n      \"pmids\": [\"25361606\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological extracellular substrates in vivo not defined\", \"Regulation of the secretory decision unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identifying DNAJB11 as a determinant of ERAD routing for disease-variant clients (mutant GCase, ZAAT) linked the chaperone to degradative triage decisions.\",\n      \"evidence\": \"IP-MS interaction, siRNA depletion, and pathway-redirection/degradation assays in patient-derived cells\",\n      \"pmids\": [\"25126989\", \"28419579\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect ERAD targeting not fully separated\", \"Single-lab characterization per client\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovering the native tetramer (dimer of dimers) via domains II/III redefined the functional unit beyond canonical HSP40 dimers.\",\n      \"evidence\": \"EM structural modeling with domain-deletion mutagenesis and functional assays\",\n      \"pmids\": [\"28655754\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"High-resolution structure not obtained\", \"Dynamics of oligomer interconversion unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Linking DNAJB11 loss to defective maturation of polycystin-1 and uromodulin connected its chaperone activity to human kidney disease clients.\",\n      \"evidence\": \"DNAJB11-null cells and affected human kidney tissue with trafficking/maturation assays\",\n      \"pmids\": [\"29706351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal in vivo mechanism not yet established\", \"Whether PC1 or UMOD defect drives disease unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defining the ERdj3\\u2013SDF2/SDF2L1 complex explained ER retention and an enhanced, BiP-independent chaperone mode.\",\n      \"evidence\": \"In vitro reconstitution, aggregation suppression with denatured GST, co-IP, and localization analysis\",\n      \"pmids\": [\"31624144\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural detail of the complex not resolved\", \"Switch between tetramer and SDF2L1-bound state not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mouse models established that DNAJB11 kidney disease arises from a PC1-specific GPS cleavage defect on the ADPKD spectrum, distinct from ADTKD/UPR mechanisms.\",\n      \"evidence\": \"Germline and conditional knockout mice, null cell lines, PC1 cleavage and UPR-marker assays\",\n      \"pmids\": [\"37332102\", \"39530576\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular step of GPS cleavage facilitation not defined\", \"Why PC1 is uniquely sensitive unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identifying ATM phosphorylation of T188 revealed a DNA-damage-responsive, substrate-specific chaperone function for \\u03b1-synuclein delivery to HSP70.\",\n      \"evidence\": \"Phosphoproteomics, T188 mutagenesis, co-chaperone delivery and neurite outgrowth assays\",\n      \"pmids\": [\"41256008\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How an ER co-chaperone accesses cytoplasmic ATM signaling unclear\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Validating SDF2/SDF2L1 as essential PC1-processing cofactors and RFFL as the degradative ligase tied the chaperone complex and its turnover to disease-relevant client processing.\",\n      \"evidence\": \"AP-MS, CRISPR knockouts with PC1 processing/rescue, label-free MS, and in vivo ubiquitination assays\",\n      \"pmids\": [\"41109348\", \"40568870\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"RFFL regulation of DNAJB11 in physiological/disease contexts not established\", \"Whether SDF2/SDF2L1 directly contact PC1 unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DNAJB11 mechanistically facilitates the specific GPS autoproteolytic cleavage of polycystin-1, and how this is integrated with its tetramer/SDF2L1 states, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of DNAJB11 with PC1 or SDF2L1\", \"Molecular basis of PC1 client selectivity unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [0, 1, 6, 13, 17]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 5, 11]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 5, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 10, 17]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 5, 11]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [2, 4, 13]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [12, 14, 16, 18, 21]}\n    ],\n    \"complexes\": [\n      \"ERdj3\\u2013SDF2\\u2013SDF2L1 complex\",\n      \"ERdj3 homotetramer (dimer of dimers)\"\n    ],\n    \"partners\": [\n      \"HSPA5\",\n      \"SDF2L1\",\n      \"SDF2\",\n      \"SEC61A1\",\n      \"RFFL\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":9,"faith_total":9,"faith_pct":100.0}}