{"gene":"PSMD3","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":1999,"finding":"Yeast Rpn3 (ortholog of PSMD3) is an essential non-ATPase subunit of the 19S regulatory particle required for ubiquitin-dependent proteolysis of specific cell cycle regulators: conditional inactivation of Rpn3 caused metaphase arrest and stabilized SCF substrate Cln2, Clb5, and APC/C substrates Clb2 and Pds1, but did not affect Sic1 turnover — demonstrating that distinct 19S subunits are required for proteolysis of specific substrates.","method":"Temperature-sensitive rpn3 mutant alleles in budding yeast; cell cycle analysis; substrate half-life measurements (pulse-chase); genetic epistasis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean conditional loss-of-function with multiple defined substrate readouts, replicated across several substrates in a single rigorous study with multiple orthogonal methods","pmids":["10490625"],"is_preprint":false},{"year":2011,"finding":"Yeast Rpn3 (PSMD3 ortholog) directly binds Rpn11 (a proteasome-associated deubiquitinating enzyme); rpn3 mutants show reduced assembly of intact 26S proteasomes (decreased 19S–20S association), destabilization of Rpn11, failure to recruit Rpn11 into mature proteasomes, reduced proteasome interaction with shuttle factor Rad23, accumulation of multiUb-protein conjugates on Rad23, and stabilization of proteolytic substrates.","method":"Co-immunoprecipitation (Rpn3–Rpn11 interaction); native gel / glycerol gradient fractionation of proteasome complexes; protein stability assays; Rad23-binding assays; genetic depletion of Rpn11 in rpn3 background","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assays, proteasome assembly fractionation, and proteolytic substrate stabilization across multiple orthogonal methods in a single study","pmids":["21619884"],"is_preprint":false},{"year":2019,"finding":"PSMD3 physically interacts with HER2 protein, stabilizing it from ubiquitin-mediated degradation; knockdown of PSMD3 in HER2+ breast cancer cells enhanced HER2 ubiquitination, reduced HER2 protein levels, and redirected HER2 toward lysosomal degradation (evidenced by LAMP-1 accumulation at the membrane and decreased HER2 immunostaining).","method":"Co-immunoprecipitation (PSMD3–HER2 interaction); siRNA-mediated PSMD3 knockdown; ubiquitination assay; LAMP-1 immunostaining/localization; western blot; colony formation and apoptosis assays","journal":"Cancers","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus functional ubiquitination assay and localization readout, single lab with multiple orthogonal methods","pmids":["31013812"],"is_preprint":false},{"year":2021,"finding":"PSMD3 (and PSMD1) promote NF-κB protein expression and nuclear activity in CML cells; knockdown of PSMD3 reduced NF-κB levels, decreased cell survival, and increased apoptosis in CML cells, implicating PSMD3 in stabilizing NF-κB through the 19S proteasome regulatory complex.","method":"shRNA/siRNA knockdown; luciferase NF-κB reporter assay; immunoblot; nucleocytoplasmic fractionation; apoptosis assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assay plus fractionation and immunoblot with loss-of-function, single lab with two orthogonal functional readouts","pmids":["33712704"],"is_preprint":false},{"year":2023,"finding":"PSMD3 interacts with ILF3 protein in lung cancer cells and stabilizes ILF3 by promoting its deubiquitination, thereby preventing ILF3 proteasomal degradation; PSMD3 knockdown reduced ILF3 protein stability and suppressed lung cancer cell proliferation, migration, and invasion.","method":"Co-IP followed by mass spectrometry (PSMD3 binding partners); cycloheximide (CHX) chase protein stability assay; ubiquitination assay; immunofluorescence co-localization; siRNA knockdown; xenograft tumor model","journal":"Biology direct","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP/MS identification plus CHX chase and ubiquitination assay, single lab with multiple orthogonal methods","pmids":["37337223"],"is_preprint":false},{"year":2026,"finding":"The metabolite OAA (2-oxoindole-3-acetate) directly binds PSMD3 in intestinal cells, leading to destabilization of the m6A-binding protein YTHDF2; loss of YTHDF2 derepressed Rxrb mRNA, increasing CD36 and FABP2 expression and promoting intestinal lipid absorption.","method":"Biotin-labeled OAA pull-down coupled with proteomics; in vitro and in vivo validation; loss-of-function assays for YTHDF2","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — chemical pulldown with proteomics plus in vitro/in vivo functional validation, single lab","pmids":["41844893"],"is_preprint":false},{"year":2023,"finding":"PSMD3 mutations (c.689T>C; p.F230S and c.1015C>A; p.L339M) reduce PSMD3 mRNA and protein expression and cause apoptosis of human retinal pigment epithelial cells; knock-in mice carrying the point mutation showed significantly increased ocular axial length, linking PSMD3 loss-of-function to pathological myopia development.","method":"Exome/Sanger sequencing; RT-qPCR; immunofluorescence; annexin V/7AAD flow cytometry apoptosis assay; CRISPR knock-in mouse model with ocular biometry","journal":"Journal of medical genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knock-in mouse model plus cell-based apoptosis assay with defined molecular readout, single lab","pmids":["36948574"],"is_preprint":false}],"current_model":"PSMD3 (Rpn3) is an essential non-ATPase subunit of the 19S regulatory particle of the 26S proteasome that is required for proteasome assembly and integrity (via stabilizing Rpn11 incorporation), enables ubiquitin-dependent proteolysis of specific substrates (cell cycle regulators, NF-κB, HER2, ILF3) by facilitating multiubiquitin-conjugate processing, and can be functionally modulated by direct binding of the metabolite OAA, with loss-of-function mutations causing apoptosis of retinal cells and axial eye elongation."},"narrative":{"mechanistic_narrative":"PSMD3 (Rpn3) is an essential non-ATPase subunit of the 19S regulatory particle of the 26S proteasome required for ubiquitin-dependent proteolysis of specific substrates [PMID:10490625]. It is integral to proteasome assembly and integrity: PSMD3 directly binds the deubiquitinating subunit Rpn11, stabilizes it, and is needed for its incorporation into mature proteasomes, so that loss of PSMD3 impairs 19S–20S association, reduces proteasome engagement of the shuttle factor Rad23, and causes accumulation of multiubiquitin-protein conjugates and stabilization of proteolytic substrates [PMID:21619884]. Through this control over substrate turnover, PSMD3 selectively governs the proteolysis of cell cycle regulators (SCF and APC/C substrates) [PMID:10490625] and stabilizes a set of oncogenic clients—HER2 [PMID:31013812], NF-κB [PMID:33712704], and ILF3 [PMID:37337223]—by limiting their ubiquitin-dependent degradation, with knockdown redirecting HER2 toward lysosomal degradation and reducing NF-κB nuclear activity and cancer-cell survival [PMID:31013812, PMID:33712704, PMID:37337223]. PSMD3 is also a binding target of the metabolite OAA, which destabilizes the m6A-reader YTHDF2 to derepress Rxrb and promote intestinal lipid absorption [PMID:41844893]. Loss-of-function PSMD3 point mutations reduce its expression, trigger apoptosis of retinal pigment epithelial cells, and increase ocular axial length in knock-in mice, linking PSMD3 to pathological myopia [PMID:36948574].","teleology":[{"year":1999,"claim":"Established that a specific 19S subunit is not a generic proteolysis factor but is selectively required for degradation of defined substrates, distinguishing substrate-specific from substrate-general roles within the regulatory particle.","evidence":"Temperature-sensitive rpn3 alleles in budding yeast with cell-cycle analysis and pulse-chase substrate half-life measurements","pmids":["10490625"],"confidence":"High","gaps":["Does not define the structural basis by which Rpn3 confers substrate selectivity","Mechanism distinguishing Sic1-independent from Cln2/Clb-dependent processing unresolved","Human PSMD3 not directly tested in this study"]},{"year":2011,"claim":"Answered how Rpn3 contributes to proteasome function mechanistically, showing it acts as an assembly determinant that recruits and stabilizes the deubiquitinase Rpn11 into intact 26S particles.","evidence":"Reciprocal Co-IP, native gel/glycerol-gradient fractionation, protein stability and Rad23-binding assays in yeast","pmids":["21619884"],"confidence":"High","gaps":["Atomic interface between Rpn3 and Rpn11 not resolved","Whether human PSMD3 stabilizes the human Rpn11 ortholog not tested here"]},{"year":2019,"claim":"Extended PSMD3 function to client-protein stabilization in cancer, showing PSMD3 physically protects HER2 from ubiquitin-mediated and lysosomal degradation.","evidence":"Reciprocal Co-IP, siRNA knockdown, ubiquitination assay, and LAMP-1 localization in HER2+ breast cancer cells","pmids":["31013812"],"confidence":"Medium","gaps":["Whether stabilization is direct or via general proteasome assembly defect not separated","Single lab; no in vivo confirmation of HER2 stabilization"]},{"year":2021,"claim":"Showed PSMD3 sustains NF-κB protein levels and nuclear activity, linking proteasome subunit function to a survival-signaling output in leukemia cells.","evidence":"shRNA/siRNA knockdown, NF-κB luciferase reporter, nucleocytoplasmic fractionation and apoptosis assays in CML cells","pmids":["33712704"],"confidence":"Medium","gaps":["Direct physical interaction between PSMD3 and NF-κB not demonstrated","Mechanism of NF-κB stabilization versus general proteostasis effect unresolved"]},{"year":2023,"claim":"Identified ILF3 as a PSMD3-stabilized client, with PSMD3 promoting ILF3 deubiquitination to support tumor cell proliferation and invasion.","evidence":"Co-IP/MS, CHX-chase stability and ubiquitination assays, immunofluorescence co-localization, knockdown and xenograft model in lung cancer","pmids":["37337223"],"confidence":"Medium","gaps":["Whether ILF3 deubiquitination is mediated through the Rpn11-PSMD3 axis not established","Single lab"]},{"year":2023,"claim":"Connected PSMD3 loss-of-function to a defined disease phenotype, showing point mutations reduce PSMD3 expression, cause retinal cell apoptosis, and increase ocular axial length.","evidence":"Exome/Sanger sequencing, RT-qPCR, apoptosis flow cytometry, and CRISPR knock-in mouse with ocular biometry","pmids":["36948574"],"confidence":"Medium","gaps":["Molecular link between reduced PSMD3 and axial elongation not mechanistically traced","Single family/lab"]},{"year":2026,"claim":"Revealed a non-canonical regulatory input, showing the metabolite OAA directly binds PSMD3 to destabilize YTHDF2 and reprogram intestinal lipid absorption.","evidence":"Biotin-OAA pull-down with proteomics plus in vitro and in vivo YTHDF2 loss-of-function validation in intestinal cells","pmids":["41844893"],"confidence":"Medium","gaps":["Structural binding site of OAA on PSMD3 not mapped","How OAA binding mechanistically alters YTHDF2 stability unresolved","Single lab"]},{"year":null,"claim":"How PSMD3 achieves substrate-selective stabilization versus degradation, and whether its cancer clients and OAA-dependent regulation operate through the same Rpn11-coupled assembly mechanism, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of human PSMD3 within the 19S particle in the corpus","Unclear whether client stabilization is direct binding or indirect via proteasome integrity","Mechanistic unification of metabolic, oncogenic, and ocular roles not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[1]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,4]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0]}],"complexes":["26S proteasome 19S regulatory particle"],"partners":["PSMD14","RAD23","HER2","ILF3","PSMD1","YTHDF2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O43242","full_name":"26S proteasome non-ATPase regulatory subunit 3","aliases":["26S proteasome regulatory subunit RPN3","26S proteasome regulatory subunit S3","Proteasome subunit p58"],"length_aa":534,"mass_kda":61.0,"function":"Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/O43242/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PSMD3","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000108344","cell_line_id":"CID000119","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":3}],"interactors":[{"gene":"PSMA1","stoichiometry":10.0},{"gene":"PSMA2","stoichiometry":10.0},{"gene":"PSMA3","stoichiometry":10.0},{"gene":"PSMA4","stoichiometry":10.0},{"gene":"PSMA6","stoichiometry":10.0},{"gene":"PSMB1","stoichiometry":10.0},{"gene":"PSMB2","stoichiometry":10.0},{"gene":"PSMB3","stoichiometry":10.0},{"gene":"PSMB4","stoichiometry":10.0},{"gene":"PSMB5","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000119","total_profiled":1310},"omim":[{"mim_id":"617858","title":"PROTEASOME INHIBITOR SUBUNIT 1; PSMF1","url":"https://www.omim.org/entry/617858"},{"mim_id":"617676","title":"PROTEASOME 26S SUBUNIT, NON-ATPase, 3; PSMD3","url":"https://www.omim.org/entry/617676"},{"mim_id":"610935","title":"ZINC-ACTIVATED ION CHANNEL; ZACN","url":"https://www.omim.org/entry/610935"},{"mim_id":"312180","title":"UBIQUITIN-CONJUGATING ENZYME E2 A; UBE2A","url":"https://www.omim.org/entry/312180"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":242.1}],"url":"https://www.proteinatlas.org/search/PSMD3"},"hgnc":{"alias_symbol":["S3","P58","Rpn3"],"prev_symbol":["TSTA2"]},"alphafold":{"accession":"O43242","domains":[{"cath_id":"-","chopping":"69-138_159-222","consensus_level":"medium","plddt":71.7555,"start":69,"end":222},{"cath_id":"1.10.10.10","chopping":"415-467","consensus_level":"high","plddt":84.8902,"start":415,"end":467}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O43242","model_url":"https://alphafold.ebi.ac.uk/files/AF-O43242-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O43242-F1-predicted_aligned_error_v6.png","plddt_mean":72.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PSMD3","jax_strain_url":"https://www.jax.org/strain/search?query=PSMD3"},"sequence":{"accession":"O43242","fasta_url":"https://rest.uniprot.org/uniprotkb/O43242.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O43242/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O43242"}},"corpus_meta":[{"pmid":"31013812","id":"PMC_31013812","title":"Proteasome 26S Subunit, non-ATPase 3 (PSMD3) Regulates Breast Cancer by Stabilizing HER2 from Degradation.","date":"2019","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/31013812","citation_count":38,"is_preprint":false},{"pmid":"10490625","id":"PMC_10490625","title":"Functional characterization of rpn3 uncovers a distinct 19S proteasomal subunit requirement for ubiquitin-dependent proteolysis of cell cycle regulatory proteins in budding yeast.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10490625","citation_count":37,"is_preprint":false},{"pmid":"33712704","id":"PMC_33712704","title":"Proteasome 26S subunit, non-ATPases 1 (PSMD1) and 3 (PSMD3), play an oncogenic role in chronic myeloid leukemia by stabilizing nuclear factor-kappa B.","date":"2021","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/33712704","citation_count":34,"is_preprint":false},{"pmid":"21619884","id":"PMC_21619884","title":"A proteasome assembly defect in rpn3 mutants is associated with Rpn11 instability and increased sensitivity to stress.","date":"2011","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/21619884","citation_count":17,"is_preprint":false},{"pmid":"23303871","id":"PMC_23303871","title":"Genetic variants at PSMD3 interact with dietary fat and carbohydrate to modulate insulin resistance.","date":"2013","source":"The Journal of nutrition","url":"https://pubmed.ncbi.nlm.nih.gov/23303871","citation_count":15,"is_preprint":false},{"pmid":"37337223","id":"PMC_37337223","title":"PSMD3-ILF3 signaling cascade drives lung cancer cell proliferation and migration.","date":"2023","source":"Biology direct","url":"https://pubmed.ncbi.nlm.nih.gov/37337223","citation_count":11,"is_preprint":false},{"pmid":"25515861","id":"PMC_25515861","title":"Genome-wide association study identifies a PSMD3 variant associated with neutropenia in interferon-based therapy for chronic hepatitis C.","date":"2014","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25515861","citation_count":10,"is_preprint":false},{"pmid":"36948574","id":"PMC_36948574","title":"PSMD3 gene mutations cause pathological myopia.","date":"2023","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36948574","citation_count":5,"is_preprint":false},{"pmid":"41844893","id":"PMC_41844893","title":"Romboutsia ilealis related metabolite OAA controls obesity and lipid metabolism through PSMD3-mediated degradation of YTHDF2.","date":"2026","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/41844893","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.01.16.633339","title":"A systems genetics approach identifies roles for proteasome factors in heart development and congenital heart defects","date":"2025-01-21","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.16.633339","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7824,"output_tokens":2024,"usd":0.026916,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8993,"output_tokens":2929,"usd":0.059095,"stage2_stop_reason":"end_turn"},"total_usd":0.086011,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"Yeast Rpn3 (ortholog of PSMD3) is an essential non-ATPase subunit of the 19S regulatory particle required for ubiquitin-dependent proteolysis of specific cell cycle regulators: conditional inactivation of Rpn3 caused metaphase arrest and stabilized SCF substrate Cln2, Clb5, and APC/C substrates Clb2 and Pds1, but did not affect Sic1 turnover — demonstrating that distinct 19S subunits are required for proteolysis of specific substrates.\",\n      \"method\": \"Temperature-sensitive rpn3 mutant alleles in budding yeast; cell cycle analysis; substrate half-life measurements (pulse-chase); genetic epistasis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean conditional loss-of-function with multiple defined substrate readouts, replicated across several substrates in a single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"10490625\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Yeast Rpn3 (PSMD3 ortholog) directly binds Rpn11 (a proteasome-associated deubiquitinating enzyme); rpn3 mutants show reduced assembly of intact 26S proteasomes (decreased 19S–20S association), destabilization of Rpn11, failure to recruit Rpn11 into mature proteasomes, reduced proteasome interaction with shuttle factor Rad23, accumulation of multiUb-protein conjugates on Rad23, and stabilization of proteolytic substrates.\",\n      \"method\": \"Co-immunoprecipitation (Rpn3–Rpn11 interaction); native gel / glycerol gradient fractionation of proteasome complexes; protein stability assays; Rad23-binding assays; genetic depletion of Rpn11 in rpn3 background\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assays, proteasome assembly fractionation, and proteolytic substrate stabilization across multiple orthogonal methods in a single study\",\n      \"pmids\": [\"21619884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PSMD3 physically interacts with HER2 protein, stabilizing it from ubiquitin-mediated degradation; knockdown of PSMD3 in HER2+ breast cancer cells enhanced HER2 ubiquitination, reduced HER2 protein levels, and redirected HER2 toward lysosomal degradation (evidenced by LAMP-1 accumulation at the membrane and decreased HER2 immunostaining).\",\n      \"method\": \"Co-immunoprecipitation (PSMD3–HER2 interaction); siRNA-mediated PSMD3 knockdown; ubiquitination assay; LAMP-1 immunostaining/localization; western blot; colony formation and apoptosis assays\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus functional ubiquitination assay and localization readout, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"31013812\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PSMD3 (and PSMD1) promote NF-κB protein expression and nuclear activity in CML cells; knockdown of PSMD3 reduced NF-κB levels, decreased cell survival, and increased apoptosis in CML cells, implicating PSMD3 in stabilizing NF-κB through the 19S proteasome regulatory complex.\",\n      \"method\": \"shRNA/siRNA knockdown; luciferase NF-κB reporter assay; immunoblot; nucleocytoplasmic fractionation; apoptosis assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assay plus fractionation and immunoblot with loss-of-function, single lab with two orthogonal functional readouts\",\n      \"pmids\": [\"33712704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PSMD3 interacts with ILF3 protein in lung cancer cells and stabilizes ILF3 by promoting its deubiquitination, thereby preventing ILF3 proteasomal degradation; PSMD3 knockdown reduced ILF3 protein stability and suppressed lung cancer cell proliferation, migration, and invasion.\",\n      \"method\": \"Co-IP followed by mass spectrometry (PSMD3 binding partners); cycloheximide (CHX) chase protein stability assay; ubiquitination assay; immunofluorescence co-localization; siRNA knockdown; xenograft tumor model\",\n      \"journal\": \"Biology direct\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP/MS identification plus CHX chase and ubiquitination assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"37337223\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The metabolite OAA (2-oxoindole-3-acetate) directly binds PSMD3 in intestinal cells, leading to destabilization of the m6A-binding protein YTHDF2; loss of YTHDF2 derepressed Rxrb mRNA, increasing CD36 and FABP2 expression and promoting intestinal lipid absorption.\",\n      \"method\": \"Biotin-labeled OAA pull-down coupled with proteomics; in vitro and in vivo validation; loss-of-function assays for YTHDF2\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — chemical pulldown with proteomics plus in vitro/in vivo functional validation, single lab\",\n      \"pmids\": [\"41844893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PSMD3 mutations (c.689T>C; p.F230S and c.1015C>A; p.L339M) reduce PSMD3 mRNA and protein expression and cause apoptosis of human retinal pigment epithelial cells; knock-in mice carrying the point mutation showed significantly increased ocular axial length, linking PSMD3 loss-of-function to pathological myopia development.\",\n      \"method\": \"Exome/Sanger sequencing; RT-qPCR; immunofluorescence; annexin V/7AAD flow cytometry apoptosis assay; CRISPR knock-in mouse model with ocular biometry\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knock-in mouse model plus cell-based apoptosis assay with defined molecular readout, single lab\",\n      \"pmids\": [\"36948574\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PSMD3 (Rpn3) is an essential non-ATPase subunit of the 19S regulatory particle of the 26S proteasome that is required for proteasome assembly and integrity (via stabilizing Rpn11 incorporation), enables ubiquitin-dependent proteolysis of specific substrates (cell cycle regulators, NF-κB, HER2, ILF3) by facilitating multiubiquitin-conjugate processing, and can be functionally modulated by direct binding of the metabolite OAA, with loss-of-function mutations causing apoptosis of retinal cells and axial eye elongation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PSMD3 (Rpn3) is an essential non-ATPase subunit of the 19S regulatory particle of the 26S proteasome required for ubiquitin-dependent proteolysis of specific substrates [#0]. It is integral to proteasome assembly and integrity: PSMD3 directly binds the deubiquitinating subunit Rpn11, stabilizes it, and is needed for its incorporation into mature proteasomes, so that loss of PSMD3 impairs 19S\\u201320S association, reduces proteasome engagement of the shuttle factor Rad23, and causes accumulation of multiubiquitin-protein conjugates and stabilization of proteolytic substrates [#1]. Through this control over substrate turnover, PSMD3 selectively governs the proteolysis of cell cycle regulators (SCF and APC/C substrates) [#0] and stabilizes a set of oncogenic clients\\u2014HER2 [#2], NF-\\u03baB [#3], and ILF3 [#4]\\u2014by limiting their ubiquitin-dependent degradation, with knockdown redirecting HER2 toward lysosomal degradation and reducing NF-\\u03baB nuclear activity and cancer-cell survival [#2, #3, #4]. PSMD3 is also a binding target of the metabolite OAA, which destabilizes the m6A-reader YTHDF2 to derepress Rxrb and promote intestinal lipid absorption [#5]. Loss-of-function PSMD3 point mutations reduce its expression, trigger apoptosis of retinal pigment epithelial cells, and increase ocular axial length in knock-in mice, linking PSMD3 to pathological myopia [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established that a specific 19S subunit is not a generic proteolysis factor but is selectively required for degradation of defined substrates, distinguishing substrate-specific from substrate-general roles within the regulatory particle.\",\n      \"evidence\": \"Temperature-sensitive rpn3 alleles in budding yeast with cell-cycle analysis and pulse-chase substrate half-life measurements\",\n      \"pmids\": [\"10490625\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not define the structural basis by which Rpn3 confers substrate selectivity\",\n        \"Mechanism distinguishing Sic1-independent from Cln2/Clb-dependent processing unresolved\",\n        \"Human PSMD3 not directly tested in this study\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Answered how Rpn3 contributes to proteasome function mechanistically, showing it acts as an assembly determinant that recruits and stabilizes the deubiquitinase Rpn11 into intact 26S particles.\",\n      \"evidence\": \"Reciprocal Co-IP, native gel/glycerol-gradient fractionation, protein stability and Rad23-binding assays in yeast\",\n      \"pmids\": [\"21619884\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic interface between Rpn3 and Rpn11 not resolved\",\n        \"Whether human PSMD3 stabilizes the human Rpn11 ortholog not tested here\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended PSMD3 function to client-protein stabilization in cancer, showing PSMD3 physically protects HER2 from ubiquitin-mediated and lysosomal degradation.\",\n      \"evidence\": \"Reciprocal Co-IP, siRNA knockdown, ubiquitination assay, and LAMP-1 localization in HER2+ breast cancer cells\",\n      \"pmids\": [\"31013812\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether stabilization is direct or via general proteasome assembly defect not separated\",\n        \"Single lab; no in vivo confirmation of HER2 stabilization\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed PSMD3 sustains NF-\\u03baB protein levels and nuclear activity, linking proteasome subunit function to a survival-signaling output in leukemia cells.\",\n      \"evidence\": \"shRNA/siRNA knockdown, NF-\\u03baB luciferase reporter, nucleocytoplasmic fractionation and apoptosis assays in CML cells\",\n      \"pmids\": [\"33712704\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct physical interaction between PSMD3 and NF-\\u03baB not demonstrated\",\n        \"Mechanism of NF-\\u03baB stabilization versus general proteostasis effect unresolved\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified ILF3 as a PSMD3-stabilized client, with PSMD3 promoting ILF3 deubiquitination to support tumor cell proliferation and invasion.\",\n      \"evidence\": \"Co-IP/MS, CHX-chase stability and ubiquitination assays, immunofluorescence co-localization, knockdown and xenograft model in lung cancer\",\n      \"pmids\": [\"37337223\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether ILF3 deubiquitination is mediated through the Rpn11-PSMD3 axis not established\",\n        \"Single lab\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected PSMD3 loss-of-function to a defined disease phenotype, showing point mutations reduce PSMD3 expression, cause retinal cell apoptosis, and increase ocular axial length.\",\n      \"evidence\": \"Exome/Sanger sequencing, RT-qPCR, apoptosis flow cytometry, and CRISPR knock-in mouse with ocular biometry\",\n      \"pmids\": [\"36948574\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular link between reduced PSMD3 and axial elongation not mechanistically traced\",\n        \"Single family/lab\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Revealed a non-canonical regulatory input, showing the metabolite OAA directly binds PSMD3 to destabilize YTHDF2 and reprogram intestinal lipid absorption.\",\n      \"evidence\": \"Biotin-OAA pull-down with proteomics plus in vitro and in vivo YTHDF2 loss-of-function validation in intestinal cells\",\n      \"pmids\": [\"41844893\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Structural binding site of OAA on PSMD3 not mapped\",\n        \"How OAA binding mechanistically alters YTHDF2 stability unresolved\",\n        \"Single lab\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PSMD3 achieves substrate-selective stabilization versus degradation, and whether its cancer clients and OAA-dependent regulation operate through the same Rpn11-coupled assembly mechanism, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of human PSMD3 within the 19S particle in the corpus\",\n        \"Unclear whether client stabilization is direct binding or indirect via proteasome integrity\",\n        \"Mechanistic unification of metabolic, oncogenic, and ocular roles not established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"26S proteasome 19S regulatory particle\"\n    ],\n    \"partners\": [\n      \"PSMD14\",\n      \"RAD23\",\n      \"HER2\",\n      \"ILF3\",\n      \"PSMD1\",\n      \"YTHDF2\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}