{"gene":"VBP1","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":1996,"finding":"VBP1 (VBP-1) directly binds to pVHL in vivo; the interaction requires the C-terminal end of pVHL (a C-terminal 26-amino acid deletion abolishes binding). Co-immunoprecipitation confirmed complex formation in cells. When VBP1 is expressed alone it localizes to the cytoplasm, but co-expression with VHL causes VBP1 to translocate to the nucleus, indicating VHL controls VBP1 subcellular localization.","method":"Yeast two-hybrid screen, co-immunoprecipitation/Western blot, fluorescence localization with VHL co-expression","journal":"Cancer Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP confirmed binding in vivo, deletion mapping defined binding region, localization experiment; single lab but multiple orthogonal methods","pmids":["8674032"],"is_preprint":false},{"year":2003,"finding":"VBP-1 is required for embryonic morphogenesis in C. elegans; RNAi knockdown of vbp-1 causes embryonic arrest at the morula stage, demonstrating an essential role in early development.","method":"dsRNA interference (RNAi) in C. elegans with embryonic arrest phenotype readout","journal":"Oncology Reports","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean loss-of-function with defined developmental phenotype in an ortholog model, single lab, single method","pmids":["12579260"],"is_preprint":false},{"year":2008,"finding":"VBP1 physically interacts with hepatitis B virus X protein (HBx) both in vitro and in vivo, and VBP1 facilitates HBx-induced NF-κB activation and cell proliferation.","method":"Yeast two-hybrid, co-immunoprecipitation (in vitro and in vivo), NF-κB reporter assay, cell proliferation assay","journal":"BMB Reports","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP confirmed interaction in two systems, functional NF-κB reporter assay; single lab","pmids":["18315953"],"is_preprint":false},{"year":2013,"finding":"VBP1 targets the meiotic DNA repair protein hMSH4 for proteasome- and autophagy-mediated degradation via polyubiquitination. VBP1 recruits p97 (an AAA+ ATPase) as a new binding partner; VBP1, VHL, and p97 co-exist in the hMSH4 immunocomplex and together regulate hMSH4 polyubiquitination and degradation.","method":"Co-immunoprecipitation, ubiquitination assay, proteasome/autophagy inhibitor treatments, knockdown experiments in HEK293T cells","journal":"FASEB Journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, ubiquitination assay, multiple inhibitor conditions; single lab with orthogonal approaches","pmids":["23964080"],"is_preprint":false},{"year":2017,"finding":"VBP1 enhances the stability of pVHL and facilitates pVHL-mediated ubiquitination and degradation of HIF-1α, thereby suppressing HIF-1α-induced epithelial-mesenchymal transition in vitro and tumor metastasis in vivo.","method":"Co-immunoprecipitation, ubiquitination assay, protein stability assay, EMT assay in vitro, in vivo metastasis model","journal":"The FEBS Journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, in vitro and in vivo functional readouts; single lab","pmids":["29121446"],"is_preprint":false},{"year":2020,"finding":"VBP1 directly binds all four TCF/LEF family transcription factors and pVHL; either overexpression or knockdown of VBP1 increases the TCF/LEF–pVHL association and promotes proteasomal degradation of TCF/LEFs, thereby decreasing Wnt/β-catenin signaling activity in cultured cells and zebrafish embryos.","method":"Co-immunoprecipitation, protein stability/proteasome inhibitor assay, Wnt reporter assay, zebrafish embryo in vivo experiments, VBP1 knockdown and overexpression","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, proteasomal degradation assay, reporter assay, and in vivo zebrafish validation; single lab with multiple orthogonal methods","pmids":["32989053"],"is_preprint":false},{"year":2023,"finding":"VBP1 negatively regulates HIF-1α (but not HIF-2α) in a pVHL-independent manner by interacting with the ubiquitin ligase CHIP and HSP70; VBP1 negatively regulates CHIP stability and facilitates CHIP-mediated ubiquitination and degradation of HIF-1α. Deletion of vbp1 in zebrafish causes Hif-1α accumulation and upregulation of Hif target genes, and promotes hematopoietic stem cell induction under hypoxia.","method":"Co-immunoprecipitation (VBP1–CHIP, VBP1–HSP70), ubiquitination assay, zebrafish vbp1 knockout with gene expression readout, in vitro cell culture HIF-1α degradation assay","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP identifying new binding partners, ubiquitination assay, pVHL-independent mechanism validated in zebrafish KO and in vitro; multiple orthogonal methods with in vivo confirmation","pmids":["37201586"],"is_preprint":false}],"current_model":"VBP1 (PFDN3/PFD3) is a cytoplasmic protein that binds pVHL via the VHL C-terminus, enhances pVHL stability and pVHL-mediated ubiquitination of HIF-1α, and also promotes HIF-1α degradation independently of pVHL through recruitment of the ubiquitin ligase CHIP and its co-chaperone HSP70; additionally, VBP1 controls the stability of TCF/LEF transcription factors by bridging them to pVHL for proteasomal degradation (modulating Wnt/β-catenin signaling), targets hMSH4 for degradation in complex with pVHL and p97, interacts with HBx to facilitate NF-κB activation, and is essential for embryonic morphogenesis in C. elegans."},"narrative":{"mechanistic_narrative":"VBP1 is a cytoplasmic protein that functions as an adaptor coupling its binding partners to the ubiquitin-proteasome system, thereby controlling the stability of multiple regulatory proteins [PMID:8674032, PMID:29121446, PMID:37201586]. It was first identified as a direct pVHL-binding protein, with the interaction requiring the C-terminal end of pVHL; pVHL co-expression drives VBP1 from the cytoplasm into the nucleus, indicating that pVHL controls VBP1 localization [PMID:8674032]. Through its pVHL association, VBP1 enhances pVHL stability and facilitates pVHL-mediated ubiquitination and degradation of HIF-1α, suppressing HIF-1α-driven epithelial-mesenchymal transition and tumor metastasis [PMID:29121446]. VBP1 also drives HIF-1α degradation independently of pVHL by interacting with the ubiquitin ligase CHIP and the co-chaperone HSP70, regulating CHIP stability and promoting CHIP-mediated HIF-1α ubiquitination; loss of vbp1 in zebrafish causes Hif-1α accumulation, Hif target-gene upregulation, and enhanced hematopoietic stem cell induction under hypoxia [PMID:37201586]. Beyond hypoxia signaling, VBP1 broadens this degradation-adaptor role: it bridges all four TCF/LEF transcription factors to pVHL to promote their proteasomal degradation, dampening Wnt/β-catenin signaling [PMID:32989053], and recruits the AAA+ ATPase p97 together with pVHL to target the meiotic DNA repair protein hMSH4 for polyubiquitination and degradation [PMID:23964080]. VBP1 additionally interacts with hepatitis B virus X protein to facilitate HBx-induced NF-κB activation and cell proliferation [PMID:18315953], and is required for early embryonic morphogenesis in C. elegans, where vbp-1 knockdown arrests embryos at the morula stage [PMID:12579260].","teleology":[{"year":1996,"claim":"Established VBP1 as a direct physical partner of the VHL tumor suppressor and showed that pVHL governs VBP1's nucleocytoplasmic distribution, placing VBP1 in the VHL functional orbit.","evidence":"Yeast two-hybrid, reciprocal co-IP, and deletion mapping of the pVHL C-terminus with localization assay upon VHL co-expression","pmids":["8674032"],"confidence":"Medium","gaps":["Did not define the catalytic/functional consequence of the VBP1-pVHL complex","Mechanism of pVHL-driven nuclear translocation of VBP1 unresolved"]},{"year":2003,"claim":"Demonstrated that VBP1 has an essential organismal function beyond protein binding, being required for early embryonic development.","evidence":"RNAi knockdown of vbp-1 in C. elegans scored for embryonic arrest at the morula stage","pmids":["12579260"],"confidence":"Medium","gaps":["Molecular pathway underlying the morphogenesis defect not identified","Single method in an ortholog model without molecular mechanism"]},{"year":2008,"claim":"Connected VBP1 to viral signaling, showing it interacts with HBx and contributes to NF-κB-driven proliferation.","evidence":"Yeast two-hybrid, co-IP in vitro and in vivo, NF-κB reporter and proliferation assays","pmids":["18315953"],"confidence":"Medium","gaps":["Whether VBP1 acts via its degradation-adaptor activity in this context is unknown","Single lab; no in vivo infection model"]},{"year":2013,"claim":"Defined VBP1 as a degradation adaptor that, with pVHL and the AAA+ ATPase p97, targets a specific substrate (hMSH4) for polyubiquitination and turnover.","evidence":"Reciprocal co-IP, ubiquitination assay, proteasome/autophagy inhibitor and knockdown experiments in HEK293T cells","pmids":["23964080"],"confidence":"Medium","gaps":["The responsible E3 ligase was not identified","Physiological relevance of hMSH4 turnover in meiosis not tested in vivo"]},{"year":2017,"claim":"Showed VBP1 stabilizes pVHL and promotes pVHL-mediated HIF-1α degradation, linking it to suppression of EMT and metastasis.","evidence":"Co-IP, ubiquitination and protein stability assays, in vitro EMT assays, and an in vivo metastasis model","pmids":["29121446"],"confidence":"Medium","gaps":["Mechanism by which VBP1 stabilizes pVHL not defined","Did not distinguish HIF-1α versus HIF-2α selectivity"]},{"year":2020,"claim":"Extended the bridging-for-degradation model to Wnt signaling, with VBP1 coupling TCF/LEF factors to pVHL for proteasomal degradation.","evidence":"Co-IP, proteasome inhibitor stability assays, Wnt reporter assays, and zebrafish embryo overexpression/knockdown","pmids":["32989053"],"confidence":"Medium","gaps":["Identity of the E3 ligase in TCF/LEF turnover unresolved","Why both overexpression and knockdown increase the TCF/LEF-pVHL association is unexplained"]},{"year":2023,"claim":"Resolved a pVHL-independent route for HIF-1α control, showing VBP1 engages CHIP and HSP70 to degrade HIF-1α specifically, with organismal consequences for hypoxia-driven hematopoiesis.","evidence":"Co-IP mapping VBP1-CHIP and VBP1-HSP70, ubiquitination assays, in vitro HIF-1α degradation, and zebrafish vbp1 knockout with target-gene and HSC readouts","pmids":["37201586"],"confidence":"High","gaps":["Structural basis for VBP1's choice between pVHL- and CHIP-dependent routes not defined","How VBP1 selectively regulates HIF-1α but not HIF-2α is unknown"]},{"year":null,"claim":"It remains unknown what unifies VBP1's role as a degradation adaptor across diverse substrates and how its activity is regulated to select among pVHL-dependent and pVHL-independent pathways.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of VBP1 in any of its complexes","Determinants of substrate and E3-ligase selectivity uncharacterized","Endogenous regulation of VBP1 expression/activity unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,5,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4,6]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[],"complexes":[],"partners":["VHL","HIF1A","CHIP","HSPA1A","P97","TCF7","HMSH4","HBX"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P61758","full_name":"Prefoldin subunit 3","aliases":["HIBBJ46","von Hippel-Lindau-binding protein 1","VBP-1","VHL-binding protein 1"],"length_aa":197,"mass_kda":22.6,"function":"Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/P61758/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/VBP1","classification":"Common Essential","n_dependent_lines":862,"n_total_lines":1208,"dependency_fraction":0.7135761589403974},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PFDN6","stoichiometry":10.0},{"gene":"CCT2","stoichiometry":0.2},{"gene":"CLINT1","stoichiometry":0.2},{"gene":"GDI1","stoichiometry":0.2},{"gene":"MAP4","stoichiometry":0.2},{"gene":"TUBA1B","stoichiometry":0.2},{"gene":"TUBB4B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/VBP1","total_profiled":1310},"omim":[{"mim_id":"604897","title":"PREFOLDIN 1; PFDN1","url":"https://www.omim.org/entry/604897"},{"mim_id":"603135","title":"CULLIN 2; CUL2","url":"https://www.omim.org/entry/603135"},{"mim_id":"308300","title":"INCONTINENTIA PIGMENTI; IP","url":"https://www.omim.org/entry/308300"},{"mim_id":"300815","title":"CHROMOSOME Xq28 DUPLICATION SYNDROME","url":"https://www.omim.org/entry/300815"},{"mim_id":"300133","title":"VON HIPPEL-LINDAU BINDING PROTEIN 1; VBP1","url":"https://www.omim.org/entry/300133"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VBP1"},"hgnc":{"alias_symbol":["PFD3","PFDN3"],"prev_symbol":[]},"alphafold":{"accession":"P61758","domains":[{"cath_id":"1.10.287.370","chopping":"43-183","consensus_level":"high","plddt":94.0559,"start":43,"end":183}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P61758","model_url":"https://alphafold.ebi.ac.uk/files/AF-P61758-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P61758-F1-predicted_aligned_error_v6.png","plddt_mean":86.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VBP1","jax_strain_url":"https://www.jax.org/strain/search?query=VBP1"},"sequence":{"accession":"P61758","fasta_url":"https://rest.uniprot.org/uniprotkb/P61758.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P61758/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P61758"}},"corpus_meta":[{"pmid":"8674032","id":"PMC_8674032","title":"Identification of a novel protein (VBP-1) binding to the von Hippel-Lindau (VHL) tumor suppressor gene product.","date":"1996","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/8674032","citation_count":106,"is_preprint":false},{"pmid":"18315953","id":"PMC_18315953","title":"Hepatitis B virus X protein enhances NFkappaB activity through cooperating with VBP1.","date":"2008","source":"BMB reports","url":"https://pubmed.ncbi.nlm.nih.gov/18315953","citation_count":40,"is_preprint":false},{"pmid":"29121446","id":"PMC_29121446","title":"VBP1 represses cancer metastasis by enhancing HIF-1α degradation induced by pVHL.","date":"2017","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/29121446","citation_count":29,"is_preprint":false},{"pmid":"9339366","id":"PMC_9339366","title":"Characterization of the gene (VBP1) and transcript for the von Hippel-Lindau binding protein and isolation of the highly conserved murine homologue.","date":"1997","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/9339366","citation_count":24,"is_preprint":false},{"pmid":"23964080","id":"PMC_23964080","title":"VBP1 facilitates proteasome and autophagy-mediated degradation of MutS homologue hMSH4.","date":"2013","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/23964080","citation_count":20,"is_preprint":false},{"pmid":"10441001","id":"PMC_10441001","title":"Genomic organization and chromosomal localization of the human CUL2 gene and the role of von Hippel-Lindau tumor suppressor-binding protein (CUL2 and VBP1) mutation and loss in renal-cell carcinoma development.","date":"1999","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/10441001","citation_count":18,"is_preprint":false},{"pmid":"32989053","id":"PMC_32989053","title":"VBP1 modulates Wnt/β-catenin signaling by mediating the stability of the transcription factors TCF/LEFs.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32989053","citation_count":17,"is_preprint":false},{"pmid":"37201586","id":"PMC_37201586","title":"VBP1 negatively regulates CHIP and selectively inhibits the activity of hypoxia-inducible factor (HIF)-1α but not HIF-2α.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37201586","citation_count":14,"is_preprint":false},{"pmid":"9931330","id":"PMC_9931330","title":"Expression of the von Hippel-Lindau-binding protein-1 (Vbp1) in fetal and adult mouse tissues.","date":"1999","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/9931330","citation_count":8,"is_preprint":false},{"pmid":"38700744","id":"PMC_38700744","title":"VBP1 promotes tumor proliferation as a part of the hypoxia-related signature in esophageal squamous cell carcinoma.","date":"2024","source":"Human cell","url":"https://pubmed.ncbi.nlm.nih.gov/38700744","citation_count":4,"is_preprint":false},{"pmid":"12579260","id":"PMC_12579260","title":"VBP-1 is necessary for morphogenesis in Caenorhabditis elegans.","date":"2003","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/12579260","citation_count":4,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7228,"output_tokens":1916,"usd":0.025212,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8844,"output_tokens":2877,"usd":0.058072,"stage2_stop_reason":"end_turn"},"total_usd":0.083284,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"VBP1 (VBP-1) directly binds to pVHL in vivo; the interaction requires the C-terminal end of pVHL (a C-terminal 26-amino acid deletion abolishes binding). Co-immunoprecipitation confirmed complex formation in cells. When VBP1 is expressed alone it localizes to the cytoplasm, but co-expression with VHL causes VBP1 to translocate to the nucleus, indicating VHL controls VBP1 subcellular localization.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation/Western blot, fluorescence localization with VHL co-expression\",\n      \"journal\": \"Cancer Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP confirmed binding in vivo, deletion mapping defined binding region, localization experiment; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"8674032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"VBP-1 is required for embryonic morphogenesis in C. elegans; RNAi knockdown of vbp-1 causes embryonic arrest at the morula stage, demonstrating an essential role in early development.\",\n      \"method\": \"dsRNA interference (RNAi) in C. elegans with embryonic arrest phenotype readout\",\n      \"journal\": \"Oncology Reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean loss-of-function with defined developmental phenotype in an ortholog model, single lab, single method\",\n      \"pmids\": [\"12579260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"VBP1 physically interacts with hepatitis B virus X protein (HBx) both in vitro and in vivo, and VBP1 facilitates HBx-induced NF-κB activation and cell proliferation.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation (in vitro and in vivo), NF-κB reporter assay, cell proliferation assay\",\n      \"journal\": \"BMB Reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP confirmed interaction in two systems, functional NF-κB reporter assay; single lab\",\n      \"pmids\": [\"18315953\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"VBP1 targets the meiotic DNA repair protein hMSH4 for proteasome- and autophagy-mediated degradation via polyubiquitination. VBP1 recruits p97 (an AAA+ ATPase) as a new binding partner; VBP1, VHL, and p97 co-exist in the hMSH4 immunocomplex and together regulate hMSH4 polyubiquitination and degradation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, proteasome/autophagy inhibitor treatments, knockdown experiments in HEK293T cells\",\n      \"journal\": \"FASEB Journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, ubiquitination assay, multiple inhibitor conditions; single lab with orthogonal approaches\",\n      \"pmids\": [\"23964080\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"VBP1 enhances the stability of pVHL and facilitates pVHL-mediated ubiquitination and degradation of HIF-1α, thereby suppressing HIF-1α-induced epithelial-mesenchymal transition in vitro and tumor metastasis in vivo.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, protein stability assay, EMT assay in vitro, in vivo metastasis model\",\n      \"journal\": \"The FEBS Journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, in vitro and in vivo functional readouts; single lab\",\n      \"pmids\": [\"29121446\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"VBP1 directly binds all four TCF/LEF family transcription factors and pVHL; either overexpression or knockdown of VBP1 increases the TCF/LEF–pVHL association and promotes proteasomal degradation of TCF/LEFs, thereby decreasing Wnt/β-catenin signaling activity in cultured cells and zebrafish embryos.\",\n      \"method\": \"Co-immunoprecipitation, protein stability/proteasome inhibitor assay, Wnt reporter assay, zebrafish embryo in vivo experiments, VBP1 knockdown and overexpression\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, proteasomal degradation assay, reporter assay, and in vivo zebrafish validation; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"32989053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"VBP1 negatively regulates HIF-1α (but not HIF-2α) in a pVHL-independent manner by interacting with the ubiquitin ligase CHIP and HSP70; VBP1 negatively regulates CHIP stability and facilitates CHIP-mediated ubiquitination and degradation of HIF-1α. Deletion of vbp1 in zebrafish causes Hif-1α accumulation and upregulation of Hif target genes, and promotes hematopoietic stem cell induction under hypoxia.\",\n      \"method\": \"Co-immunoprecipitation (VBP1–CHIP, VBP1–HSP70), ubiquitination assay, zebrafish vbp1 knockout with gene expression readout, in vitro cell culture HIF-1α degradation assay\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP identifying new binding partners, ubiquitination assay, pVHL-independent mechanism validated in zebrafish KO and in vitro; multiple orthogonal methods with in vivo confirmation\",\n      \"pmids\": [\"37201586\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VBP1 (PFDN3/PFD3) is a cytoplasmic protein that binds pVHL via the VHL C-terminus, enhances pVHL stability and pVHL-mediated ubiquitination of HIF-1α, and also promotes HIF-1α degradation independently of pVHL through recruitment of the ubiquitin ligase CHIP and its co-chaperone HSP70; additionally, VBP1 controls the stability of TCF/LEF transcription factors by bridging them to pVHL for proteasomal degradation (modulating Wnt/β-catenin signaling), targets hMSH4 for degradation in complex with pVHL and p97, interacts with HBx to facilitate NF-κB activation, and is essential for embryonic morphogenesis in C. elegans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VBP1 is a cytoplasmic protein that functions as an adaptor coupling its binding partners to the ubiquitin-proteasome system, thereby controlling the stability of multiple regulatory proteins [#0, #4, #6]. It was first identified as a direct pVHL-binding protein, with the interaction requiring the C-terminal end of pVHL; pVHL co-expression drives VBP1 from the cytoplasm into the nucleus, indicating that pVHL controls VBP1 localization [#0]. Through its pVHL association, VBP1 enhances pVHL stability and facilitates pVHL-mediated ubiquitination and degradation of HIF-1\\u03b1, suppressing HIF-1\\u03b1-driven epithelial-mesenchymal transition and tumor metastasis [#4]. VBP1 also drives HIF-1\\u03b1 degradation independently of pVHL by interacting with the ubiquitin ligase CHIP and the co-chaperone HSP70, regulating CHIP stability and promoting CHIP-mediated HIF-1\\u03b1 ubiquitination; loss of vbp1 in zebrafish causes Hif-1\\u03b1 accumulation, Hif target-gene upregulation, and enhanced hematopoietic stem cell induction under hypoxia [#6]. Beyond hypoxia signaling, VBP1 broadens this degradation-adaptor role: it bridges all four TCF/LEF transcription factors to pVHL to promote their proteasomal degradation, dampening Wnt/\\u03b2-catenin signaling [#5], and recruits the AAA+ ATPase p97 together with pVHL to target the meiotic DNA repair protein hMSH4 for polyubiquitination and degradation [#3]. VBP1 additionally interacts with hepatitis B virus X protein to facilitate HBx-induced NF-\\u03baB activation and cell proliferation [#2], and is required for early embryonic morphogenesis in C. elegans, where vbp-1 knockdown arrests embryos at the morula stage [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Established VBP1 as a direct physical partner of the VHL tumor suppressor and showed that pVHL governs VBP1's nucleocytoplasmic distribution, placing VBP1 in the VHL functional orbit.\",\n      \"evidence\": \"Yeast two-hybrid, reciprocal co-IP, and deletion mapping of the pVHL C-terminus with localization assay upon VHL co-expression\",\n      \"pmids\": [\"8674032\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the catalytic/functional consequence of the VBP1-pVHL complex\", \"Mechanism of pVHL-driven nuclear translocation of VBP1 unresolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstrated that VBP1 has an essential organismal function beyond protein binding, being required for early embryonic development.\",\n      \"evidence\": \"RNAi knockdown of vbp-1 in C. elegans scored for embryonic arrest at the morula stage\",\n      \"pmids\": [\"12579260\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular pathway underlying the morphogenesis defect not identified\", \"Single method in an ortholog model without molecular mechanism\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Connected VBP1 to viral signaling, showing it interacts with HBx and contributes to NF-\\u03baB-driven proliferation.\",\n      \"evidence\": \"Yeast two-hybrid, co-IP in vitro and in vivo, NF-\\u03baB reporter and proliferation assays\",\n      \"pmids\": [\"18315953\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether VBP1 acts via its degradation-adaptor activity in this context is unknown\", \"Single lab; no in vivo infection model\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined VBP1 as a degradation adaptor that, with pVHL and the AAA+ ATPase p97, targets a specific substrate (hMSH4) for polyubiquitination and turnover.\",\n      \"evidence\": \"Reciprocal co-IP, ubiquitination assay, proteasome/autophagy inhibitor and knockdown experiments in HEK293T cells\",\n      \"pmids\": [\"23964080\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The responsible E3 ligase was not identified\", \"Physiological relevance of hMSH4 turnover in meiosis not tested in vivo\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showed VBP1 stabilizes pVHL and promotes pVHL-mediated HIF-1\\u03b1 degradation, linking it to suppression of EMT and metastasis.\",\n      \"evidence\": \"Co-IP, ubiquitination and protein stability assays, in vitro EMT assays, and an in vivo metastasis model\",\n      \"pmids\": [\"29121446\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which VBP1 stabilizes pVHL not defined\", \"Did not distinguish HIF-1\\u03b1 versus HIF-2\\u03b1 selectivity\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended the bridging-for-degradation model to Wnt signaling, with VBP1 coupling TCF/LEF factors to pVHL for proteasomal degradation.\",\n      \"evidence\": \"Co-IP, proteasome inhibitor stability assays, Wnt reporter assays, and zebrafish embryo overexpression/knockdown\",\n      \"pmids\": [\"32989053\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the E3 ligase in TCF/LEF turnover unresolved\", \"Why both overexpression and knockdown increase the TCF/LEF-pVHL association is unexplained\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolved a pVHL-independent route for HIF-1\\u03b1 control, showing VBP1 engages CHIP and HSP70 to degrade HIF-1\\u03b1 specifically, with organismal consequences for hypoxia-driven hematopoiesis.\",\n      \"evidence\": \"Co-IP mapping VBP1-CHIP and VBP1-HSP70, ubiquitination assays, in vitro HIF-1\\u03b1 degradation, and zebrafish vbp1 knockout with target-gene and HSC readouts\",\n      \"pmids\": [\"37201586\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for VBP1's choice between pVHL- and CHIP-dependent routes not defined\", \"How VBP1 selectively regulates HIF-1\\u03b1 but not HIF-2\\u03b1 is unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown what unifies VBP1's role as a degradation adaptor across diverse substrates and how its activity is regulated to select among pVHL-dependent and pVHL-independent pathways.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of VBP1 in any of its complexes\", \"Determinants of substrate and E3-ligase selectivity uncharacterized\", \"Endogenous regulation of VBP1 expression/activity unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 5, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008953897\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"VHL\", \"HIF1A\", \"CHIP\", \"HSPA1A\", \"p97\", \"TCF7\", \"hMSH4\", \"HBx\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}