{"gene":"UBXN6","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2023,"finding":"UBXD1 acts as a potent p97 ATPase inhibitor and drives asymmetric remodeling of the p97 hexamer into a ring-open conformation. Cryo-EM structures of intact p97-UBXD1 complexes reveal that conserved VIM, UBX, and PUB domains tether adjacent p97 protomers, while a connecting strand forms an N-terminal domain lariat with a helix wedged at the interprotomer interface, and an additional VIM-connecting helix binds along the D2 AAA+ domain.","method":"Cryo-EM structure determination, mutagenesis, ATPase activity assays","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure of intact complex, mutagenesis, and in vitro ATPase assays in a single rigorous study; independently corroborated by preprint (PMID:37292947)","pmids":["37945741","37292947"],"is_preprint":false},{"year":2011,"finding":"VCP/p97 cooperates with UBXD1 to target mono-ubiquitylated caveolin-1 (CAV1) in high-molecular-weight complexes on endosomes, mediating its sorting for degradation in endolysosomes. VCP disease mutations specifically disrupt the VCP-UBXD1 complex, and siRNA depletion of UBXD1 blocks CAV1 transport at the limiting membrane of enlarged endosomes.","method":"Mass spectrometry (unbiased interactome), co-immunoprecipitation, siRNA knockdown, live-cell imaging, patient muscle tissue analysis","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, MS identification, siRNA with defined cellular phenotype, and patient tissue validation; multiple orthogonal methods in one study","pmids":["21822278"],"is_preprint":false},{"year":2016,"finding":"Upon lysosomal damage, p97 translocates to lysosomes and cooperates with UBXD1, PLAA, and the deubiquitinase YOD1 (the ELDR complex) downstream of K63-linked ubiquitination and p62 recruitment to selectively remove K48-linked ubiquitin conjugates from damaged lysosomes, thereby promoting autophagosome formation and clearance of ruptured lysosomes.","method":"siRNA knockdown, co-immunoprecipitation, immunofluorescence localization, lysosomal damage assays (LLOMe treatment), MEF models with p97 disease mutations","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, siRNA, cell biology, patient/MEF models), replicated across conditions","pmids":["27753622"],"is_preprint":false},{"year":2008,"finding":"UBXD1 is a p97 cofactor that does not associate with p97 via its UBX domain but instead via its PUB domain, which binds the extreme C-terminus of p97. Phosphorylation of the penultimate tyrosine in p97 completely abolishes UBXD1 interaction. Ternary complexes of UBXD1, p47, and p97 were detected in vitro. UBXD1 localizes to the cytoplasm, nucleus, and is highly enriched at centrosomes.","method":"Co-immunoprecipitation, in vitro binding assays, siRNA knockdown, immunofluorescence, phosphorylation mutagenesis","journal":"The international journal of biochemistry & cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, in vitro binding, localization, and mutagenesis in single lab with multiple orthogonal methods","pmids":["18656546"],"is_preprint":false},{"year":2009,"finding":"UBXD1 binds p97 through two independent sites: the PUB domain mediates robust binding to the C-terminus of p97, while the UBX domain does not contribute to p97 binding. An additional binding site in UBXD1 competes with the p47 cofactor for the p97 N-domain, suggesting a bipartite binding mode that could regulate cofactor interactions.","method":"Biochemical binding assays, co-immunoprecipitation in living cells, domain deletion analysis","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical and cell-based assays with domain mutants, single lab, two orthogonal approaches","pmids":["19174149"],"is_preprint":false},{"year":2009,"finding":"UBXD1 is a cytosolic protein that interacts with VCP and Derlin-1 and is involved in ERAD. Overexpression of UBXD1 causes selective dissociation of Ufd1 from VCP, inhibiting degradation of mutant CFTR. Conversely, siRNA-mediated depletion of UBXD1 also impairs CFTR degradation, indicating UBXD1 is a regulatory component of ERAD that modulates adaptor binding to VCP.","method":"Co-immunoprecipitation, overexpression, siRNA knockdown, CFTR degradation assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional ERAD assay with both gain- and loss-of-function, single lab","pmids":["19275885"],"is_preprint":false},{"year":2016,"finding":"VCP cooperates with UBXD1 to degrade the mitochondrial outer membrane protein MCL1 in a Huntington's disease context. UBXD1 selectively binds MCL1 and interacts with VCP to mediate MCL1 extraction from mitochondria; VCP translocates to mitochondria and promotes MCL1 degradation, which is abolished by VCP RNAi or dominant-negative VCP.","method":"Co-immunoprecipitation, RNAi knockdown, dominant-negative VCP expression, immunofluorescence, HD cell culture models","journal":"Biochimica et biophysica acta. Molecular basis of disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, RNAi, dominant-negative with defined substrate degradation readout; single lab","pmids":["27913212"],"is_preprint":false},{"year":2015,"finding":"The intrinsically disordered N-terminal region of UBXD1 (UBXD1-N) binds to both the p97 N-domain and N/D1 interface (including disease-associated residues) and additionally contacts the D1D2 barrel. UBXD1-N binding reduces p97 ATPase activity and partially protects p97 from proteolysis, indicating that UBXD1-N intercalates into the p97 ND1 interface to modulate interdomain communication.","method":"NMR titration, CD spectroscopy, fluorescence anisotropy, cell-based endosomal localization assays, domain mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structural mapping, mutagenesis, and functional ATPase assay with multiple orthogonal biophysical methods in single rigorous study","pmids":["26475856"],"is_preprint":false},{"year":2019,"finding":"The NMR solution structure of the UBXD1 PUB domain was determined. Binding studies and mutational analysis defined its interaction with the p97 C-terminus; the binding pocket is conserved among PUB domains, but UBXD1-PUB features unique loop and turn regions.","method":"NMR structure determination, binding studies, mutational analysis","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR structure with mutagenesis but functional consequence of unique structural features not directly established; single lab","pmids":["31847414"],"is_preprint":false},{"year":2012,"finding":"UBXD1 associates with ERGIC-53 through its N-terminal 10 residues binding the C-terminal cytoplasmic 12 amino acids of ERGIC-53. Complex formation requires p97 ATPase activity but not ubiquitin modification. UBXD1 modulates the sub-cellular trafficking of ERGIC-53, including promoting its movement to the cell membrane. UBXD1 also associates with Rab3GAP1/2 in an ERGIC-53-dependent manner.","method":"LC-MS/MS interactome profiling, SILAC quantitative proteomics, co-immunoprecipitation/Western blot, p97 inhibitor treatment, E1 enzyme inhibitor, localization studies","journal":"Molecular & cellular proteomics : MCP","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS interactome plus Co-IP validation plus localization with domain mapping; single lab","pmids":["22337587"],"is_preprint":false},{"year":2022,"finding":"In Torsin-deficient cells, p97/UBXD1 activity is required to generate K48-ubiquitylated proteins that are sequestered into nuclear envelope herniations (blebs). This activity does not significantly depend on the Ufd1/Npl4 heterodimer. p97 inhibition abrogates K48-ubiquitin accumulation in blebs, implicating the p97/UBXD1 axis in DYT1 dystonia pathology.","method":"p97 inhibitor treatment, UBXD1 knockdown, Ufd1/Npl4 knockdown, immunofluorescence quantification of K48-ubiquitin in nuclear envelope blebs","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function (inhibitor + RNAi) with defined cellular phenotype; single lab, multiple conditions","pmids":["35563018"],"is_preprint":false},{"year":2019,"finding":"UBXN6 knockdown in HeLa-P4 cells and macrophages causes increased CAV1 expression and its accumulation at the plasma membrane, confirming UBXN6's role in CAV1 turnover. UBXN6 knockdown also increases HIV-1 replication capacity in vitro.","method":"siRNA knockdown, flow cytometry/immunofluorescence for CAV1, HIV-1 in vitro replication assay","journal":"Clinical microbiology and infection","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method per readout, no mechanistic pathway placement beyond confirming CAV1 phenotype","pmids":["31158522"],"is_preprint":false}],"current_model":"UBXN6/UBXD1 is a multi-domain adaptor for the AAA+ ATPase p97/VCP that binds p97 through at least three interfaces (an intrinsically disordered N-terminal region engaging the N-domain and N/D1 interface, a VIM motif, a UBX domain, and a PUB domain binding the p97 C-terminus), collectively inhibiting p97 ATPase activity and driving asymmetric ring-opening of the hexamer; it recruits p97 to specific substrates including mono-ubiquitylated caveolin-1 on endosomes (directing its endolysosomal degradation), MCL1 on the mitochondrial outer membrane, and damaged lysosomes (as part of the ELDR complex with YOD1 and PLAA to remove K48-ubiquitin and promote selective autophagy), while also modulating ERAD and ERGIC-53 trafficking, with p97 disease mutations specifically disrupting the p97-UBXD1 interaction and impairing these pathways."},"narrative":{"mechanistic_narrative":"UBXN6/UBXD1 is a multi-domain cofactor of the AAA+ ATPase p97/VCP that couples p97 to selective protein extraction and organelle quality-control pathways [PMID:21822278, PMID:27753622]. It engages p97 through multiple interfaces: a PUB domain that binds the extreme C-terminus of p97 (an interaction abolished by phosphorylation of the penultimate tyrosine) [PMID:18656546, PMID:31847414], an intrinsically disordered N-terminal region that intercalates into the p97 N-domain and N/D1 interface and contacts the D1D2 barrel [PMID:26475856], and VIM and UBX elements that tether adjacent protomers [PMID:21822278]; notably the UBX domain itself does not mediate p97 binding [PMID:19174149]. Through these contacts UBXD1 acts as a potent ATPase inhibitor that drives asymmetric remodeling of the p97 hexamer into a ring-open conformation [PMID:21822278], and it competes with the p47 and Ufd1 adaptors for p97, thereby reconfiguring cofactor occupancy [PMID:19174149, PMID:19275885]. Functionally, UBXD1 directs p97 to specific substrates and membranes: it targets mono-ubiquitylated caveolin-1 in endosomal high-molecular-weight complexes for endolysosomal degradation [#1-CAV1 context, #11], extracts the mitochondrial outer-membrane protein MCL1 [PMID:27913212], and—together with PLAA and the deubiquitinase YOD1 in the ELDR complex—removes K48-linked ubiquitin conjugates from damaged lysosomes to promote selective autophagy [PMID:27753622]. It additionally modulates ERAD (regulating CFTR degradation) [PMID:19275885] and ERGIC-53 trafficking via direct N-terminal binding to the ERGIC-53 cytoplasmic tail [PMID:22337587]. p97 disease mutations specifically disrupt the p97–UBXD1 complex and impair these pathways [#1-CAV1 context], and the p97/UBXD1 axis has been implicated in DYT1 dystonia-related nuclear envelope ubiquitin accumulation [PMID:35563018].","teleology":[{"year":2008,"claim":"Established that UBXD1 is an atypical p97 cofactor that binds p97 not through its UBX domain but through its PUB domain engaging the p97 C-terminus, defining a novel mode of cofactor attachment.","evidence":"Co-IP, in vitro binding, phosphorylation mutagenesis, and immunofluorescence in cells","pmids":["18656546"],"confidence":"Medium","gaps":["Functional consequence of centrosomal enrichment not established","Physiological role of the ternary p47/UBXD1/p97 complex unresolved"]},{"year":2009,"claim":"Resolved that UBXD1 binds p97 bipartitely—via the PUB domain at the C-terminus and a separate site that competes with p47 at the N-domain—providing a mechanism for cofactor exchange regulation.","evidence":"Biochemical binding assays, cell-based Co-IP, domain deletion analysis","pmids":["19174149"],"confidence":"Medium","gaps":["Did not identify the N-domain-contacting segment structurally","Cellular substrate context not addressed"]},{"year":2009,"claim":"Connected UBXD1 to ERAD by showing it can displace Ufd1 from p97 and that both its overexpression and depletion impair mutant CFTR degradation, framing it as a regulator of which adaptors load onto p97.","evidence":"Co-IP, gain- and loss-of-function with CFTR degradation assay","pmids":["19275885"],"confidence":"Medium","gaps":["Mechanism of biphasic effect (both over- and under-expression impair) unexplained","Direct interaction with Derlin-1 not structurally mapped"]},{"year":2011,"claim":"Identified the first physiological substrate-membrane context: p97/UBXD1 sorts mono-ubiquitylated caveolin-1 on endosomes for degradation, and showed p97 disease mutations selectively disrupt the p97-UBXD1 complex.","evidence":"Unbiased MS interactome, reciprocal Co-IP, siRNA with imaging, patient muscle tissue","pmids":["21822278"],"confidence":"High","gaps":["Ubiquitin ligase generating CAV1 mono-ubiquitin not defined","How disease mutations alter complex geometry not shown structurally"]},{"year":2012,"claim":"Extended UBXD1 function to secretory trafficking by showing its N-terminal residues bind the ERGIC-53 cytoplasmic tail in a p97-ATPase-dependent but ubiquitin-independent manner, modulating ERGIC-53 distribution.","evidence":"LC-MS/MS and SILAC interactome, Co-IP, p97/E1 inhibitor treatment, localization","pmids":["22337587"],"confidence":"Medium","gaps":["Functional output of ERGIC-53 relocalization unclear","Role of Rab3GAP1/2 association undefined"]},{"year":2015,"claim":"Mapped the disordered UBXD1 N-terminal region to the p97 N-domain/N-D1 interface and D1D2 barrel, providing a structural basis for ATPase inhibition and interdomain communication control.","evidence":"NMR titration, CD, fluorescence anisotropy, mutagenesis, ATPase and proteolysis assays","pmids":["26475856"],"confidence":"High","gaps":["Did not capture the intact hexameric complex","Coupling of inhibition to substrate processing not addressed"]},{"year":2016,"claim":"Defined the ELDR complex (UBXD1, PLAA, YOD1, p97) that strips K48-ubiquitin from damaged lysosomes downstream of K63-ubiquitin/p62, linking UBXD1 to selective autophagy of ruptured lysosomes.","evidence":"siRNA, Co-IP, immunofluorescence, LLOMe lysosomal damage, p97-mutant MEFs","pmids":["27753622"],"confidence":"High","gaps":["Order of p97 recruitment relative to other ELDR subunits not fully resolved","How K48-removal triggers autophagosome formation mechanistically unclear"]},{"year":2016,"claim":"Showed UBXD1 selects MCL1 for p97-mediated extraction from the mitochondrial outer membrane, expanding UBXD1 substrate specificity to mitochondrial membrane proteins in a disease context.","evidence":"Co-IP, RNAi, dominant-negative VCP, immunofluorescence in HD cell models","pmids":["27913212"],"confidence":"Medium","gaps":["Ubiquitylation requirement for MCL1 extraction not defined","Generality beyond Huntington's disease context untested"]},{"year":2019,"claim":"Determined the NMR structure of the UBXD1 PUB domain and its p97 C-terminal binding pocket, revealing conserved binding determinants with UBXD1-specific loop features.","evidence":"NMR structure determination, binding and mutational analysis","pmids":["31847414"],"confidence":"Medium","gaps":["Functional importance of the unique loop/turn regions not established","PUB structure not placed in the context of the full complex"]},{"year":2019,"claim":"Confirmed UBXN6's role in caveolin-1 turnover in additional cell types and linked its loss to increased HIV-1 replication.","evidence":"siRNA, flow cytometry/IF for CAV1, in vitro HIV-1 replication assay","pmids":["31158522"],"confidence":"Low","gaps":["Single method per readout with no mechanistic placement of the HIV-1 effect","Whether CAV1 changes drive the HIV-1 phenotype not tested"]},{"year":2022,"claim":"Implicated the p97/UBXD1 axis, independently of Ufd1/Npl4, in generating K48-ubiquitylated proteins sequestered in nuclear envelope herniations in Torsin-deficient cells, connecting it to DYT1 dystonia pathology.","evidence":"p97 inhibitor, UBXD1 and Ufd1/Npl4 knockdown, IF quantification of K48-ubiquitin in blebs","pmids":["35563018"],"confidence":"Medium","gaps":["Direct substrates within blebs not identified","Causal contribution to dystonia phenotype not demonstrated in vivo"]},{"year":2023,"claim":"Provided the integrated structural mechanism: cryo-EM of intact p97-UBXD1 shows VIM, UBX, and PUB domains tethering adjacent protomers and an N-terminal lariat wedging at interprotomer interfaces to drive asymmetric ring-opening and ATPase inhibition.","evidence":"Cryo-EM structure of intact complex, mutagenesis, in vitro ATPase assays","pmids":["37945741","37292947"],"confidence":"High","gaps":["How ring-opening couples to substrate engagement and translocation not resolved","Conformational dynamics during active extraction not captured"]},{"year":null,"claim":"How UBXD1-driven hexamer ring-opening and ATPase inhibition are mechanistically converted into productive substrate extraction across its diverse membrane contexts (endosomes, mitochondria, lysosomes, ER) remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model linking ATPase inhibition to substrate processing","Substrate-specific recruitment determinants beyond CAV1/MCL1/ERGIC-53 undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,4,7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,5,6,9]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,5]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[2]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[6]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,9]}],"complexes":["ELDR complex (UBXD1-PLAA-YOD1-p97)","p97/VCP-UBXD1 complex"],"partners":["VCP","PLAA","YOD1","CAV1","MCL1","LMAN1","DERLIN-1","RAB3GAP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BZV1","full_name":"UBX domain-containing protein 6","aliases":["UBX domain-containing protein 1"],"length_aa":441,"mass_kda":49.8,"function":"May negatively regulate the ATPase activity of VCP, an ATP-driven segregase that associates with different cofactors to control a wide variety of cellular processes (PubMed:26475856). As a cofactor of VCP, it may play a role in the transport of CAV1 to lysosomes for degradation (PubMed:21822278, PubMed:23335559). It may also play a role in endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins (PubMed:19275885). Together with VCP and other cofactors, it may play a role in macroautophagy, regulating for instance the clearance of damaged lysosomes (PubMed:27753622)","subcellular_location":"Cytoplasm; Cytoplasm, cytosol; Membrane; Nucleus; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Early endosome membrane; Late endosome membrane; Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/Q9BZV1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBXN6","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"VCP","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/UBXN6","total_profiled":1310},"omim":[{"mim_id":"615260","title":"VALOSIN-CONTAINING PROTEIN LYSINE METHYLTRANSFERASE; VCPKMT","url":"https://www.omim.org/entry/615260"},{"mim_id":"611946","title":"UBX DOMAIN PROTEIN 6; UBXN6","url":"https://www.omim.org/entry/611946"},{"mim_id":"606236","title":"ASPSCR1 TETHER FOR SLC2A4, UBX DOMAIN-CONTAINING; ASPSCR1","url":"https://www.omim.org/entry/606236"},{"mim_id":"601023","title":"VALOSIN-CONTAINING PROTEIN; VCP","url":"https://www.omim.org/entry/601023"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBXN6"},"hgnc":{"alias_symbol":["UBXDC2"],"prev_symbol":["UBXD1"]},"alphafold":{"accession":"Q9BZV1","domains":[{"cath_id":"1.20.58.2190","chopping":"123-270","consensus_level":"high","plddt":85.2918,"start":123,"end":270},{"cath_id":"3.10.20.90","chopping":"332-440","consensus_level":"high","plddt":82.0975,"start":332,"end":440}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BZV1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BZV1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BZV1-F1-predicted_aligned_error_v6.png","plddt_mean":76.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBXN6","jax_strain_url":"https://www.jax.org/strain/search?query=UBXN6"},"sequence":{"accession":"Q9BZV1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BZV1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BZV1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BZV1"}},"corpus_meta":[{"pmid":"27753622","id":"PMC_27753622","title":"VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy.","date":"2016","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/27753622","citation_count":289,"is_preprint":false},{"pmid":"21822278","id":"PMC_21822278","title":"Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations.","date":"2011","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/21822278","citation_count":201,"is_preprint":false},{"pmid":"18656546","id":"PMC_18656546","title":"Ubxd1 is a novel co-factor of the human p97 ATPase.","date":"2008","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/18656546","citation_count":41,"is_preprint":false},{"pmid":"27913212","id":"PMC_27913212","title":"VCP cooperates with UBXD1 to degrade mitochondrial outer membrane protein MCL1 in model of Huntington's disease.","date":"2016","source":"Biochimica et biophysica acta. Molecular basis of disease","url":"https://pubmed.ncbi.nlm.nih.gov/27913212","citation_count":38,"is_preprint":false},{"pmid":"19174149","id":"PMC_19174149","title":"UBXD1 binds p97 through two independent binding sites.","date":"2009","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/19174149","citation_count":35,"is_preprint":false},{"pmid":"22337587","id":"PMC_22337587","title":"Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking.","date":"2012","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/22337587","citation_count":30,"is_preprint":false},{"pmid":"19275885","id":"PMC_19275885","title":"UBXD1 is a VCP-interacting protein that is involved in ER-associated degradation.","date":"2009","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/19275885","citation_count":29,"is_preprint":false},{"pmid":"26475856","id":"PMC_26475856","title":"The N-terminal Region of the Ubiquitin Regulatory X (UBX) Domain-containing Protein 1 (UBXD1) Modulates Interdomain Communication within the Valosin-containing Protein p97.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26475856","citation_count":26,"is_preprint":false},{"pmid":"37945741","id":"PMC_37945741","title":"The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions.","date":"2023","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/37945741","citation_count":15,"is_preprint":false},{"pmid":"11342112","id":"PMC_11342112","title":"Identification and characterization of UBXD1, a novel UBX domain-containing gene on human chromosome 19p13, and its mouse ortholog.","date":"2001","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/11342112","citation_count":13,"is_preprint":false},{"pmid":"31847414","id":"PMC_31847414","title":"Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase.","date":"2019","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/31847414","citation_count":9,"is_preprint":false},{"pmid":"35563018","id":"PMC_35563018","title":"p97/UBXD1 Generate Ubiquitylated Proteins That Are Sequestered into Nuclear Envelope Herniations in Torsin-Deficient Cells.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35563018","citation_count":6,"is_preprint":false},{"pmid":"31158522","id":"PMC_31158522","title":"Association of a single nucleotide polymorphism in the ubxn6 gene with long-term non-progression phenotype in HIV-positive individuals.","date":"2019","source":"Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases","url":"https://pubmed.ncbi.nlm.nih.gov/31158522","citation_count":4,"is_preprint":false},{"pmid":"37292947","id":"PMC_37292947","title":"The p97/VCP adapter UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37292947","citation_count":2,"is_preprint":false},{"pmid":"20025508","id":"PMC_20025508","title":"Generation and characterization of novel monoclonal antibodies recognizing UBXD1.","date":"2009","source":"Hybridoma (2005)","url":"https://pubmed.ncbi.nlm.nih.gov/20025508","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8822,"output_tokens":3350,"usd":0.038358,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10752,"output_tokens":4187,"usd":0.079217,"stage2_stop_reason":"end_turn"},"total_usd":0.117575,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"UBXD1 acts as a potent p97 ATPase inhibitor and drives asymmetric remodeling of the p97 hexamer into a ring-open conformation. Cryo-EM structures of intact p97-UBXD1 complexes reveal that conserved VIM, UBX, and PUB domains tether adjacent p97 protomers, while a connecting strand forms an N-terminal domain lariat with a helix wedged at the interprotomer interface, and an additional VIM-connecting helix binds along the D2 AAA+ domain.\",\n      \"method\": \"Cryo-EM structure determination, mutagenesis, ATPase activity assays\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure of intact complex, mutagenesis, and in vitro ATPase assays in a single rigorous study; independently corroborated by preprint (PMID:37292947)\",\n      \"pmids\": [\"37945741\", \"37292947\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"VCP/p97 cooperates with UBXD1 to target mono-ubiquitylated caveolin-1 (CAV1) in high-molecular-weight complexes on endosomes, mediating its sorting for degradation in endolysosomes. VCP disease mutations specifically disrupt the VCP-UBXD1 complex, and siRNA depletion of UBXD1 blocks CAV1 transport at the limiting membrane of enlarged endosomes.\",\n      \"method\": \"Mass spectrometry (unbiased interactome), co-immunoprecipitation, siRNA knockdown, live-cell imaging, patient muscle tissue analysis\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, MS identification, siRNA with defined cellular phenotype, and patient tissue validation; multiple orthogonal methods in one study\",\n      \"pmids\": [\"21822278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Upon lysosomal damage, p97 translocates to lysosomes and cooperates with UBXD1, PLAA, and the deubiquitinase YOD1 (the ELDR complex) downstream of K63-linked ubiquitination and p62 recruitment to selectively remove K48-linked ubiquitin conjugates from damaged lysosomes, thereby promoting autophagosome formation and clearance of ruptured lysosomes.\",\n      \"method\": \"siRNA knockdown, co-immunoprecipitation, immunofluorescence localization, lysosomal damage assays (LLOMe treatment), MEF models with p97 disease mutations\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, siRNA, cell biology, patient/MEF models), replicated across conditions\",\n      \"pmids\": [\"27753622\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"UBXD1 is a p97 cofactor that does not associate with p97 via its UBX domain but instead via its PUB domain, which binds the extreme C-terminus of p97. Phosphorylation of the penultimate tyrosine in p97 completely abolishes UBXD1 interaction. Ternary complexes of UBXD1, p47, and p97 were detected in vitro. UBXD1 localizes to the cytoplasm, nucleus, and is highly enriched at centrosomes.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assays, siRNA knockdown, immunofluorescence, phosphorylation mutagenesis\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, in vitro binding, localization, and mutagenesis in single lab with multiple orthogonal methods\",\n      \"pmids\": [\"18656546\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"UBXD1 binds p97 through two independent sites: the PUB domain mediates robust binding to the C-terminus of p97, while the UBX domain does not contribute to p97 binding. An additional binding site in UBXD1 competes with the p47 cofactor for the p97 N-domain, suggesting a bipartite binding mode that could regulate cofactor interactions.\",\n      \"method\": \"Biochemical binding assays, co-immunoprecipitation in living cells, domain deletion analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical and cell-based assays with domain mutants, single lab, two orthogonal approaches\",\n      \"pmids\": [\"19174149\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"UBXD1 is a cytosolic protein that interacts with VCP and Derlin-1 and is involved in ERAD. Overexpression of UBXD1 causes selective dissociation of Ufd1 from VCP, inhibiting degradation of mutant CFTR. Conversely, siRNA-mediated depletion of UBXD1 also impairs CFTR degradation, indicating UBXD1 is a regulatory component of ERAD that modulates adaptor binding to VCP.\",\n      \"method\": \"Co-immunoprecipitation, overexpression, siRNA knockdown, CFTR degradation assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional ERAD assay with both gain- and loss-of-function, single lab\",\n      \"pmids\": [\"19275885\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"VCP cooperates with UBXD1 to degrade the mitochondrial outer membrane protein MCL1 in a Huntington's disease context. UBXD1 selectively binds MCL1 and interacts with VCP to mediate MCL1 extraction from mitochondria; VCP translocates to mitochondria and promotes MCL1 degradation, which is abolished by VCP RNAi or dominant-negative VCP.\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, dominant-negative VCP expression, immunofluorescence, HD cell culture models\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular basis of disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, RNAi, dominant-negative with defined substrate degradation readout; single lab\",\n      \"pmids\": [\"27913212\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The intrinsically disordered N-terminal region of UBXD1 (UBXD1-N) binds to both the p97 N-domain and N/D1 interface (including disease-associated residues) and additionally contacts the D1D2 barrel. UBXD1-N binding reduces p97 ATPase activity and partially protects p97 from proteolysis, indicating that UBXD1-N intercalates into the p97 ND1 interface to modulate interdomain communication.\",\n      \"method\": \"NMR titration, CD spectroscopy, fluorescence anisotropy, cell-based endosomal localization assays, domain mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structural mapping, mutagenesis, and functional ATPase assay with multiple orthogonal biophysical methods in single rigorous study\",\n      \"pmids\": [\"26475856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The NMR solution structure of the UBXD1 PUB domain was determined. Binding studies and mutational analysis defined its interaction with the p97 C-terminus; the binding pocket is conserved among PUB domains, but UBXD1-PUB features unique loop and turn regions.\",\n      \"method\": \"NMR structure determination, binding studies, mutational analysis\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR structure with mutagenesis but functional consequence of unique structural features not directly established; single lab\",\n      \"pmids\": [\"31847414\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"UBXD1 associates with ERGIC-53 through its N-terminal 10 residues binding the C-terminal cytoplasmic 12 amino acids of ERGIC-53. Complex formation requires p97 ATPase activity but not ubiquitin modification. UBXD1 modulates the sub-cellular trafficking of ERGIC-53, including promoting its movement to the cell membrane. UBXD1 also associates with Rab3GAP1/2 in an ERGIC-53-dependent manner.\",\n      \"method\": \"LC-MS/MS interactome profiling, SILAC quantitative proteomics, co-immunoprecipitation/Western blot, p97 inhibitor treatment, E1 enzyme inhibitor, localization studies\",\n      \"journal\": \"Molecular & cellular proteomics : MCP\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS interactome plus Co-IP validation plus localization with domain mapping; single lab\",\n      \"pmids\": [\"22337587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In Torsin-deficient cells, p97/UBXD1 activity is required to generate K48-ubiquitylated proteins that are sequestered into nuclear envelope herniations (blebs). This activity does not significantly depend on the Ufd1/Npl4 heterodimer. p97 inhibition abrogates K48-ubiquitin accumulation in blebs, implicating the p97/UBXD1 axis in DYT1 dystonia pathology.\",\n      \"method\": \"p97 inhibitor treatment, UBXD1 knockdown, Ufd1/Npl4 knockdown, immunofluorescence quantification of K48-ubiquitin in nuclear envelope blebs\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function (inhibitor + RNAi) with defined cellular phenotype; single lab, multiple conditions\",\n      \"pmids\": [\"35563018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"UBXN6 knockdown in HeLa-P4 cells and macrophages causes increased CAV1 expression and its accumulation at the plasma membrane, confirming UBXN6's role in CAV1 turnover. UBXN6 knockdown also increases HIV-1 replication capacity in vitro.\",\n      \"method\": \"siRNA knockdown, flow cytometry/immunofluorescence for CAV1, HIV-1 in vitro replication assay\",\n      \"journal\": \"Clinical microbiology and infection\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method per readout, no mechanistic pathway placement beyond confirming CAV1 phenotype\",\n      \"pmids\": [\"31158522\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBXN6/UBXD1 is a multi-domain adaptor for the AAA+ ATPase p97/VCP that binds p97 through at least three interfaces (an intrinsically disordered N-terminal region engaging the N-domain and N/D1 interface, a VIM motif, a UBX domain, and a PUB domain binding the p97 C-terminus), collectively inhibiting p97 ATPase activity and driving asymmetric ring-opening of the hexamer; it recruits p97 to specific substrates including mono-ubiquitylated caveolin-1 on endosomes (directing its endolysosomal degradation), MCL1 on the mitochondrial outer membrane, and damaged lysosomes (as part of the ELDR complex with YOD1 and PLAA to remove K48-ubiquitin and promote selective autophagy), while also modulating ERAD and ERGIC-53 trafficking, with p97 disease mutations specifically disrupting the p97-UBXD1 interaction and impairing these pathways.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBXN6/UBXD1 is a multi-domain cofactor of the AAA+ ATPase p97/VCP that couples p97 to selective protein extraction and organelle quality-control pathways [#1, #2]. It engages p97 through multiple interfaces: a PUB domain that binds the extreme C-terminus of p97 (an interaction abolished by phosphorylation of the penultimate tyrosine) [#3, #8], an intrinsically disordered N-terminal region that intercalates into the p97 N-domain and N/D1 interface and contacts the D1D2 barrel [#7], and VIM and UBX elements that tether adjacent protomers [#1]; notably the UBX domain itself does not mediate p97 binding [#4]. Through these contacts UBXD1 acts as a potent ATPase inhibitor that drives asymmetric remodeling of the p97 hexamer into a ring-open conformation [#1], and it competes with the p47 and Ufd1 adaptors for p97, thereby reconfiguring cofactor occupancy [#4, #5]. Functionally, UBXD1 directs p97 to specific substrates and membranes: it targets mono-ubiquitylated caveolin-1 in endosomal high-molecular-weight complexes for endolysosomal degradation [#1-CAV1 context, #11], extracts the mitochondrial outer-membrane protein MCL1 [#6], and—together with PLAA and the deubiquitinase YOD1 in the ELDR complex—removes K48-linked ubiquitin conjugates from damaged lysosomes to promote selective autophagy [#2]. It additionally modulates ERAD (regulating CFTR degradation) [#5] and ERGIC-53 trafficking via direct N-terminal binding to the ERGIC-53 cytoplasmic tail [#9]. p97 disease mutations specifically disrupt the p97–UBXD1 complex and impair these pathways [#1-CAV1 context], and the p97/UBXD1 axis has been implicated in DYT1 dystonia-related nuclear envelope ubiquitin accumulation [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established that UBXD1 is an atypical p97 cofactor that binds p97 not through its UBX domain but through its PUB domain engaging the p97 C-terminus, defining a novel mode of cofactor attachment.\",\n      \"evidence\": \"Co-IP, in vitro binding, phosphorylation mutagenesis, and immunofluorescence in cells\",\n      \"pmids\": [\"18656546\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of centrosomal enrichment not established\", \"Physiological role of the ternary p47/UBXD1/p97 complex unresolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Resolved that UBXD1 binds p97 bipartitely—via the PUB domain at the C-terminus and a separate site that competes with p47 at the N-domain—providing a mechanism for cofactor exchange regulation.\",\n      \"evidence\": \"Biochemical binding assays, cell-based Co-IP, domain deletion analysis\",\n      \"pmids\": [\"19174149\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not identify the N-domain-contacting segment structurally\", \"Cellular substrate context not addressed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Connected UBXD1 to ERAD by showing it can displace Ufd1 from p97 and that both its overexpression and depletion impair mutant CFTR degradation, framing it as a regulator of which adaptors load onto p97.\",\n      \"evidence\": \"Co-IP, gain- and loss-of-function with CFTR degradation assay\",\n      \"pmids\": [\"19275885\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of biphasic effect (both over- and under-expression impair) unexplained\", \"Direct interaction with Derlin-1 not structurally mapped\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified the first physiological substrate-membrane context: p97/UBXD1 sorts mono-ubiquitylated caveolin-1 on endosomes for degradation, and showed p97 disease mutations selectively disrupt the p97-UBXD1 complex.\",\n      \"evidence\": \"Unbiased MS interactome, reciprocal Co-IP, siRNA with imaging, patient muscle tissue\",\n      \"pmids\": [\"21822278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin ligase generating CAV1 mono-ubiquitin not defined\", \"How disease mutations alter complex geometry not shown structurally\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Extended UBXD1 function to secretory trafficking by showing its N-terminal residues bind the ERGIC-53 cytoplasmic tail in a p97-ATPase-dependent but ubiquitin-independent manner, modulating ERGIC-53 distribution.\",\n      \"evidence\": \"LC-MS/MS and SILAC interactome, Co-IP, p97/E1 inhibitor treatment, localization\",\n      \"pmids\": [\"22337587\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional output of ERGIC-53 relocalization unclear\", \"Role of Rab3GAP1/2 association undefined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mapped the disordered UBXD1 N-terminal region to the p97 N-domain/N-D1 interface and D1D2 barrel, providing a structural basis for ATPase inhibition and interdomain communication control.\",\n      \"evidence\": \"NMR titration, CD, fluorescence anisotropy, mutagenesis, ATPase and proteolysis assays\",\n      \"pmids\": [\"26475856\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not capture the intact hexameric complex\", \"Coupling of inhibition to substrate processing not addressed\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the ELDR complex (UBXD1, PLAA, YOD1, p97) that strips K48-ubiquitin from damaged lysosomes downstream of K63-ubiquitin/p62, linking UBXD1 to selective autophagy of ruptured lysosomes.\",\n      \"evidence\": \"siRNA, Co-IP, immunofluorescence, LLOMe lysosomal damage, p97-mutant MEFs\",\n      \"pmids\": [\"27753622\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Order of p97 recruitment relative to other ELDR subunits not fully resolved\", \"How K48-removal triggers autophagosome formation mechanistically unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed UBXD1 selects MCL1 for p97-mediated extraction from the mitochondrial outer membrane, expanding UBXD1 substrate specificity to mitochondrial membrane proteins in a disease context.\",\n      \"evidence\": \"Co-IP, RNAi, dominant-negative VCP, immunofluorescence in HD cell models\",\n      \"pmids\": [\"27913212\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitylation requirement for MCL1 extraction not defined\", \"Generality beyond Huntington's disease context untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Determined the NMR structure of the UBXD1 PUB domain and its p97 C-terminal binding pocket, revealing conserved binding determinants with UBXD1-specific loop features.\",\n      \"evidence\": \"NMR structure determination, binding and mutational analysis\",\n      \"pmids\": [\"31847414\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional importance of the unique loop/turn regions not established\", \"PUB structure not placed in the context of the full complex\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Confirmed UBXN6's role in caveolin-1 turnover in additional cell types and linked its loss to increased HIV-1 replication.\",\n      \"evidence\": \"siRNA, flow cytometry/IF for CAV1, in vitro HIV-1 replication assay\",\n      \"pmids\": [\"31158522\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single method per readout with no mechanistic placement of the HIV-1 effect\", \"Whether CAV1 changes drive the HIV-1 phenotype not tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated the p97/UBXD1 axis, independently of Ufd1/Npl4, in generating K48-ubiquitylated proteins sequestered in nuclear envelope herniations in Torsin-deficient cells, connecting it to DYT1 dystonia pathology.\",\n      \"evidence\": \"p97 inhibitor, UBXD1 and Ufd1/Npl4 knockdown, IF quantification of K48-ubiquitin in blebs\",\n      \"pmids\": [\"35563018\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct substrates within blebs not identified\", \"Causal contribution to dystonia phenotype not demonstrated in vivo\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided the integrated structural mechanism: cryo-EM of intact p97-UBXD1 shows VIM, UBX, and PUB domains tethering adjacent protomers and an N-terminal lariat wedging at interprotomer interfaces to drive asymmetric ring-opening and ATPase inhibition.\",\n      \"evidence\": \"Cryo-EM structure of intact complex, mutagenesis, in vitro ATPase assays\",\n      \"pmids\": [\"37945741\", \"37292947\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How ring-opening couples to substrate engagement and translocation not resolved\", \"Conformational dynamics during active extraction not captured\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How UBXD1-driven hexamer ring-opening and ATPase inhibition are mechanistically converted into productive substrate extraction across its diverse membrane contexts (endosomes, mitochondria, lysosomes, ER) remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model linking ATPase inhibition to substrate processing\", \"Substrate-specific recruitment determinants beyond CAV1/MCL1/ERGIC-53 undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 4, 7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 5, 6, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 9]}\n    ],\n    \"complexes\": [\"ELDR complex (UBXD1-PLAA-YOD1-p97)\", \"p97/VCP-UBXD1 complex\"],\n    \"partners\": [\"VCP\", \"PLAA\", \"YOD1\", \"CAV1\", \"MCL1\", \"LMAN1\", \"Derlin-1\", \"RAB3GAP1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}