{"gene":"SNAPC3","run_date":"2026-04-28T20:42:08","timeline":{"discoveries":[{"year":1995,"finding":"SNAPc (containing SNAP43/SNAPC3, SNAP45, SNAP50, and TBP) was identified as a TBP-TAF complex that binds specifically to the proximal sequence element (PSE) and is required for transcription of both RNA polymerase II and III snRNA genes.","method":"Biochemical purification, in vitro transcription assays, DNA binding assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — original biochemical reconstitution of complex with functional transcription assays, highly cited foundational paper","pmids":["7715707"],"is_preprint":false},{"year":1996,"finding":"SNAP43 (SNAPC3) interacts with SNAP50 in co-immunoprecipitation experiments but not with SNAP45 or TBP, defining initial subunit-subunit contacts within SNAPc.","method":"Co-immunoprecipitation, antibody depletion, UV cross-linking","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP with functional depletion assays in single study","pmids":["9003788"],"is_preprint":false},{"year":1998,"finding":"SNAPc was reconstituted from five recombinant subunits — SNAP43 (SNAPC3), SNAP45, SNAP50, SNAP190, and the newly identified SNAP19 — and this recombinant complex binds specifically to the PSE and directs both RNA polymerase II and III snRNA gene transcription.","method":"Recombinant protein reconstitution, PSE binding assays, in vitro transcription","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 — full reconstitution of five-subunit complex with functional transcription, replicated across labs","pmids":["9732265"],"is_preprint":false},{"year":2000,"finding":"A detailed map of SNAPc subunit-subunit contacts was established, identifying specific domains within SNAP43 (SNAPC3), SNAP45, SNAP50, SNAP190, and SNAP19 required for subunit-subunit association; complexes containing little more than these mapped domains bind specifically to the PSE.","method":"Co-immunoprecipitation with deletion mutants, PSE binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — systematic domain mapping with multiple deletion constructs and functional PSE binding validation","pmids":["11056176"],"is_preprint":false},{"year":2002,"finding":"A mini-SNAPc containing SNAP43 (SNAPC3), SNAP50, and the N-terminal third of SNAP190 binds cooperatively with TBP to the core U6 promoter and supports RNA polymerase III transcription; SNAP43 directly interacts with the TBP DNA binding domain.","method":"TBP recruitment assays, in vitro transcription, protein interaction assays with truncation mutants","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with defined minimal complex plus direct interaction mapping","pmids":["12391172"],"is_preprint":false},{"year":2003,"finding":"SNAP43 (SNAPC3) directly interacts with the TBP DNA binding domain and is one of two SNAPc subunits (along with SNAP190) that recruit TBP to the U6 TATA box, facilitating assembly of a RNA polymerase III-specific preinitiation complex.","method":"TBP recruitment assays, direct protein interaction assays, in vitro transcription","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — direct protein interaction assays combined with functional transcription reconstitution","pmids":["12621023"],"is_preprint":false},{"year":2006,"finding":"A partial SNAPc containing SNAP190(1-505), SNAP50, SNAP43 (SNAPC3), and SNAP19 co-expressed in E. coli binds PSE DNA specifically, recruits TBP to U6 promoter DNA, and supports transcription of both U1 and U6 snRNA genes by RNA polymerases II and III.","method":"Recombinant co-expression in E. coli, DNA binding assays, TBP recruitment assays, in vitro transcription","journal":"Protein expression and purification","confidence":"High","confidence_rationale":"Tier 1 — recombinant reconstitution with functional transcription validation","pmids":["16603380"],"is_preprint":false},{"year":2022,"finding":"Cryo-EM structure of human SNAPc (N-terminal domain of SNAP190, SNAP50, and SNAP43/SNAPC3) in complex with U6-1 PSE at 3.49 Å resolution reveals a 'wrap-around' mode of PSE binding; SNAP43 is part of the stable mini-SNAPc assembly with defined three-dimensional organization.","method":"Cryo-electron microscopy structure determination at 3.49 Å resolution","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — high-resolution cryo-EM structure with functional complex validation","pmids":["36369505"],"is_preprint":false},{"year":2025,"finding":"SNAPC3 (endogenously tagged) was shown to interact with SNAPC1 in the SNAPc complex; a SUMOylation-deficient SNAPC1 mutant retains interaction with SNAPC3 but shows impaired interaction with SNAPC4, indicating SNAPC3 and SNAPC4 occupy distinct positions in the SNAPc assembly that depend on SNAPC1 SUMOylation.","method":"Endogenous tagging, co-immunoprecipitation, CRISPR/dCas9-SENP1 targeting, inducible degron system","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP with endogenous tags plus functional degron rescue system in single study","pmids":["40956881"],"is_preprint":false}],"current_model":"SNAPC3 (SNAP43) is a core subunit of the five-subunit SNAPc complex that binds the PSE promoter element of snRNA genes and nucleates assembly of both RNA polymerase II and III transcription initiation complexes; it directly contacts TBP to facilitate TBP recruitment to the TATA box, engages in specific protein-protein interactions with SNAP50 and SNAP190 within the complex, and its assembly within SNAPc is regulated by SUMOylation of the SNAPC1 subunit, as revealed by biochemical reconstitution, cryo-EM structure, and endogenous-tagging experiments."},"narrative":{"teleology":[{"year":1995,"claim":"Identification of SNAPC3 as a subunit of a novel TBP-TAF complex (SNAPc) that binds the PSE established the first molecular framework for how snRNA genes are transcribed by both RNA Pol II and Pol III.","evidence":"Biochemical purification and in vitro transcription assays from human cell extracts","pmids":["7715707"],"confidence":"High","gaps":["Individual contributions of each subunit to PSE binding were unknown","No information on subunit–subunit contacts within the complex"]},{"year":1996,"claim":"Mapping pairwise interactions showed SNAPC3 directly contacts SNAP50 but not SNAP45 or TBP, beginning to define the internal architecture of SNAPc.","evidence":"Co-immunoprecipitation and UV cross-linking in HeLa extracts","pmids":["9003788"],"confidence":"Medium","gaps":["Only pairwise interactions tested; higher-order contacts could be missed","No domain-resolution mapping of the SNAPC3–SNAP50 interface"]},{"year":1998,"claim":"Reconstitution of the complete five-subunit SNAPc from recombinant proteins demonstrated that SNAPC3 is essential for a functional complex capable of PSE binding and dual-polymerase transcription.","evidence":"Recombinant co-expression and in vitro transcription of both Pol II and Pol III snRNA templates","pmids":["9732265"],"confidence":"High","gaps":["No structure available to explain how five subunits cooperate for PSE recognition","Mechanism by which SNAPc discriminates Pol II versus Pol III promoters remained unclear"]},{"year":2000,"claim":"Systematic domain mapping identified specific regions of SNAPC3, SNAP50, and SNAP190 required for mutual association and PSE binding, showing the minimal determinants of complex assembly.","evidence":"Co-immunoprecipitation with deletion mutants and PSE EMSA","pmids":["11056176"],"confidence":"High","gaps":["Atomic-resolution contacts between domains remained undetermined","Functional contribution of individual domains to transcription not tested"]},{"year":2002,"claim":"Discovery that a mini-SNAPc containing SNAPC3, SNAP50, and the SNAP190 N-terminus directly recruits TBP to the U6 TATA box resolved how SNAPc nucleates the Pol III preinitiation complex, with SNAPC3 making direct contact with TBP's DNA-binding domain.","evidence":"TBP recruitment assays, direct protein interaction mapping, and in vitro Pol III transcription with truncation mutants","pmids":["12391172","12621023"],"confidence":"High","gaps":["Structural basis of the SNAPC3–TBP interaction unknown","Whether SNAPC3–TBP contact is also relevant for Pol II snRNA transcription was not resolved"]},{"year":2006,"claim":"Co-expression of a four-subunit partial SNAPc in E. coli confirmed that SNAPC3 is part of the minimal assembly sufficient for PSE binding, TBP recruitment, and both Pol II and Pol III transcription, validating the mini-SNAPc paradigm.","evidence":"Recombinant co-expression in E. coli with in vitro transcription of U1 and U6 templates","pmids":["16603380"],"confidence":"High","gaps":["Role of SNAP45 in the full complex assembly pathway remained structurally unresolved","Post-translational regulation of the complex was unexplored"]},{"year":2022,"claim":"A 3.49 Å cryo-EM structure of mini-SNAPc bound to U6-1 PSE revealed a wrap-around DNA-binding mode, providing the first atomic-level view of SNAPC3 within the complex and explaining how it contributes to the structural scaffold for PSE recognition.","evidence":"Cryo-EM structure determination of the human mini-SNAPc–PSE complex","pmids":["36369505"],"confidence":"High","gaps":["Structure of full five-subunit SNAPc with SNAP19 and SNAP45 not determined","SNAPC3–TBP interface not visualized structurally"]},{"year":2025,"claim":"Endogenous tagging and deSUMOylation experiments showed that SNAPC3 and SNAPC4 occupy distinct assembly positions connected through SNAPC1, and that SNAPC1 SUMOylation regulates the SNAPC1–SNAPC4 but not the SNAPC1–SNAPC3 interaction, revealing a post-translational switch governing SNAPc integrity.","evidence":"Endogenous tagging, co-immunoprecipitation, CRISPR/dCas9-SENP1 targeting, and inducible degron system in human cells","pmids":["40956881"],"confidence":"Medium","gaps":["Functional consequence of disrupted SNAPC1–SNAPC4 interaction for snRNA transcription not directly measured","Whether SUMOylation regulates SNAPc in different cell types or developmental contexts is unknown"]},{"year":null,"claim":"The structural basis of the SNAPC3–TBP interaction, the full five-subunit SNAPc structure including SNAP45 and SNAP19, and the mechanism by which SNAPc switches between Pol II and Pol III transcription modes remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure of SNAPC3–TBP interface","No complete five-subunit SNAPc structure","Mechanism of Pol II versus Pol III promoter discrimination by SNAPc is not defined at the molecular level"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,2,3,7]},{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[4,5]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[3,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2,8]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,2,4,6]}],"complexes":["SNAPc (snRNA-activating protein complex)"],"partners":["SNAPC5","SNAPC4","SNAPC2","SNAPC1","TBP"],"other_free_text":[]},"mechanistic_narrative":"SNAPC3 (SNAP43) is a core subunit of the five-subunit small nuclear RNA-activating protein complex (SNAPc), which binds the proximal sequence element (PSE) of snRNA gene promoters and is essential for transcription initiation by both RNA polymerase II and RNA polymerase III [PMID:7715707, PMID:9732265]. Within SNAPc, SNAPC3 directly contacts SNAP50 and SNAP190 to form a minimal PSE-binding subcomplex, and it additionally interacts with the DNA-binding domain of TBP to recruit TBP to the TATA box of RNA polymerase III-dependent promoters such as U6 [PMID:11056176, PMID:12621023]. A 3.49 Å cryo-EM structure of the mini-SNAPc (SNAP190 N-terminus, SNAP50, and SNAPC3) bound to the U6-1 PSE reveals a wrap-around DNA-binding architecture in which SNAPC3 is an integral structural component [PMID:36369505]. SNAPC3 occupies a position in SNAPc assembly that is distinct from SNAPC4 (SNAP45) and is connected to SNAPC1 (SNAP19) through an interaction whose broader complex integrity is regulated by SNAPC1 SUMOylation [PMID:40956881]."},"prefetch_data":{"uniprot":{"accession":"Q92966","full_name":"snRNA-activating protein complex subunit 3","aliases":["Proximal sequence element-binding transcription factor subunit beta","PSE-binding factor subunit beta","PTF subunit beta","Small nuclear RNA-activating complex polypeptide 3","snRNA-activating protein complex 50 kDa subunit","SNAPc 50 kDa subunit"],"length_aa":411,"mass_kda":46.8,"function":"Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q92966/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SNAPC3","classification":"Common Essential","n_dependent_lines":1183,"n_total_lines":1208,"dependency_fraction":0.9793046357615894},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SNAPC3","total_profiled":1310},"omim":[{"mim_id":"605979","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 5; SNAPC5","url":"https://www.omim.org/entry/605979"},{"mim_id":"602777","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 4; SNAPC4","url":"https://www.omim.org/entry/602777"},{"mim_id":"602348","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 3; SNAPC3","url":"https://www.omim.org/entry/602348"},{"mim_id":"600591","title":"SMALL NUCLEAR RNA-ACTIVATING PROTEIN COMPLEX, POLYPEPTIDE 1; SNAPC1","url":"https://www.omim.org/entry/600591"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SNAPC3"},"hgnc":{"alias_symbol":["SNAP50","PTFbeta","MGC33124","MGC132011"],"prev_symbol":[]},"alphafold":{"accession":"Q92966","domains":[{"cath_id":"3.10.290","chopping":"170-229_239-345","consensus_level":"high","plddt":91.4979,"start":170,"end":345},{"cath_id":"-","chopping":"349-411","consensus_level":"medium","plddt":92.869,"start":349,"end":411}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q92966","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q92966-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q92966-F1-predicted_aligned_error_v6.png","plddt_mean":84.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SNAPC3","jax_strain_url":"https://www.jax.org/strain/search?query=SNAPC3"},"sequence":{"accession":"Q92966","fasta_url":"https://rest.uniprot.org/uniprotkb/Q92966.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q92966/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q92966"}},"corpus_meta":[{"pmid":"7715707","id":"PMC_7715707","title":"A TBP-TAF complex required for transcription of human snRNA genes by RNA polymerase II and III.","date":"1995","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/7715707","citation_count":128,"is_preprint":false},{"pmid":"19356248","id":"PMC_19356248","title":"Histone acetylations mark origins of polycistronic transcription in Leishmania major.","date":"2009","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/19356248","citation_count":115,"is_preprint":false},{"pmid":"9418884","id":"PMC_9418884","title":"The large subunit of basal transcription factor SNAPc is a Myb domain protein that interacts with Oct-1.","date":"1998","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/9418884","citation_count":82,"is_preprint":false},{"pmid":"9732265","id":"PMC_9732265","title":"SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III.","date":"1998","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/9732265","citation_count":73,"is_preprint":false},{"pmid":"9003788","id":"PMC_9003788","title":"Cloning and characterization of SNAP50, a subunit of the snRNA-activating protein complex SNAPc.","date":"1996","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9003788","citation_count":51,"is_preprint":false},{"pmid":"16098103","id":"PMC_16098103","title":"Involvement of SRD2-mediated activation of snRNA transcription in the control of cell proliferation competence in Arabidopsis.","date":"2005","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16098103","citation_count":46,"is_preprint":false},{"pmid":"12486231","id":"PMC_12486231","title":"RNA polymerase II-dependent transcription in trypanosomes is associated with a SNAP complex-like transcription factor.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12486231","citation_count":46,"is_preprint":false},{"pmid":"31646075","id":"PMC_31646075","title":"Expression of MHC class I, HLA-A and HLA-B identifies immune-activated breast tumors with favorable outcome.","date":"2019","source":"Oncoimmunology","url":"https://pubmed.ncbi.nlm.nih.gov/31646075","citation_count":44,"is_preprint":false},{"pmid":"11056176","id":"PMC_11056176","title":"A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11056176","citation_count":41,"is_preprint":false},{"pmid":"34922489","id":"PMC_34922489","title":"Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of osteosarcoma cancer.","date":"2021","source":"BMC 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subunits enables recombinant SNAPC assembly and function for transcription by human RNA polymerases II and III.","date":"2006","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/16603380","citation_count":6,"is_preprint":false},{"pmid":"15383299","id":"PMC_15383299","title":"Failure to detect binding of Trypanosoma brucei SNAPc to U2 and U6 snRNA gene sequences by in vitro transcription competition and pull-down assays.","date":"2004","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15383299","citation_count":5,"is_preprint":false},{"pmid":"38903089","id":"PMC_38903089","title":"Integrating Genetic and Transcriptomic Data to Identify Genes Underlying Obesity Risk Loci.","date":"2024","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38903089","citation_count":2,"is_preprint":false},{"pmid":"34108018","id":"PMC_34108018","title":"TBP and SNAP50 transcription factors bind specifically to the Pr77 promoter sequence from trypanosomatid non-LTR retrotransposons.","date":"2021","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/34108018","citation_count":1,"is_preprint":false},{"pmid":"41006818","id":"PMC_41006818","title":"Integrating genetic and transcriptomic data to identify genes underlying obesity risk loci.","date":"2025","source":"International journal of obesity (2005)","url":"https://pubmed.ncbi.nlm.nih.gov/41006818","citation_count":0,"is_preprint":false},{"pmid":"40956881","id":"PMC_40956881","title":"SUMO conjugation to promoter-proximal sequence elements-associated proteins impacts on snRNA transcription.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/40956881","citation_count":0,"is_preprint":false},{"pmid":"40706988","id":"PMC_40706988","title":"A Systematic, Evidence-Based Workflow for Classifying KMT2A Fusions in Acute Myeloid Leukemia.","date":"2025","source":"The Journal of molecular diagnostics : JMD","url":"https://pubmed.ncbi.nlm.nih.gov/40706988","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13753,"output_tokens":1974,"usd":0.035435},"stage2":{"model":"claude-opus-4-6","input_tokens":5281,"output_tokens":2198,"usd":0.122033},"total_usd":0.157468,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1995,\n      \"finding\": \"SNAPc (containing SNAP43/SNAPC3, SNAP45, SNAP50, and TBP) was identified as a TBP-TAF complex that binds specifically to the proximal sequence element (PSE) and is required for transcription of both RNA polymerase II and III snRNA genes.\",\n      \"method\": \"Biochemical purification, in vitro transcription assays, DNA binding assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — original biochemical reconstitution of complex with functional transcription assays, highly cited foundational paper\",\n      \"pmids\": [\"7715707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"SNAP43 (SNAPC3) interacts with SNAP50 in co-immunoprecipitation experiments but not with SNAP45 or TBP, defining initial subunit-subunit contacts within SNAPc.\",\n      \"method\": \"Co-immunoprecipitation, antibody depletion, UV cross-linking\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with functional depletion assays in single study\",\n      \"pmids\": [\"9003788\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"SNAPc was reconstituted from five recombinant subunits — SNAP43 (SNAPC3), SNAP45, SNAP50, SNAP190, and the newly identified SNAP19 — and this recombinant complex binds specifically to the PSE and directs both RNA polymerase II and III snRNA gene transcription.\",\n      \"method\": \"Recombinant protein reconstitution, PSE binding assays, in vitro transcription\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — full reconstitution of five-subunit complex with functional transcription, replicated across labs\",\n      \"pmids\": [\"9732265\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"A detailed map of SNAPc subunit-subunit contacts was established, identifying specific domains within SNAP43 (SNAPC3), SNAP45, SNAP50, SNAP190, and SNAP19 required for subunit-subunit association; complexes containing little more than these mapped domains bind specifically to the PSE.\",\n      \"method\": \"Co-immunoprecipitation with deletion mutants, PSE binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — systematic domain mapping with multiple deletion constructs and functional PSE binding validation\",\n      \"pmids\": [\"11056176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"A mini-SNAPc containing SNAP43 (SNAPC3), SNAP50, and the N-terminal third of SNAP190 binds cooperatively with TBP to the core U6 promoter and supports RNA polymerase III transcription; SNAP43 directly interacts with the TBP DNA binding domain.\",\n      \"method\": \"TBP recruitment assays, in vitro transcription, protein interaction assays with truncation mutants\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with defined minimal complex plus direct interaction mapping\",\n      \"pmids\": [\"12391172\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"SNAP43 (SNAPC3) directly interacts with the TBP DNA binding domain and is one of two SNAPc subunits (along with SNAP190) that recruit TBP to the U6 TATA box, facilitating assembly of a RNA polymerase III-specific preinitiation complex.\",\n      \"method\": \"TBP recruitment assays, direct protein interaction assays, in vitro transcription\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct protein interaction assays combined with functional transcription reconstitution\",\n      \"pmids\": [\"12621023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"A partial SNAPc containing SNAP190(1-505), SNAP50, SNAP43 (SNAPC3), and SNAP19 co-expressed in E. coli binds PSE DNA specifically, recruits TBP to U6 promoter DNA, and supports transcription of both U1 and U6 snRNA genes by RNA polymerases II and III.\",\n      \"method\": \"Recombinant co-expression in E. coli, DNA binding assays, TBP recruitment assays, in vitro transcription\",\n      \"journal\": \"Protein expression and purification\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — recombinant reconstitution with functional transcription validation\",\n      \"pmids\": [\"16603380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cryo-EM structure of human SNAPc (N-terminal domain of SNAP190, SNAP50, and SNAP43/SNAPC3) in complex with U6-1 PSE at 3.49 Å resolution reveals a 'wrap-around' mode of PSE binding; SNAP43 is part of the stable mini-SNAPc assembly with defined three-dimensional organization.\",\n      \"method\": \"Cryo-electron microscopy structure determination at 3.49 Å resolution\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution cryo-EM structure with functional complex validation\",\n      \"pmids\": [\"36369505\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SNAPC3 (endogenously tagged) was shown to interact with SNAPC1 in the SNAPc complex; a SUMOylation-deficient SNAPC1 mutant retains interaction with SNAPC3 but shows impaired interaction with SNAPC4, indicating SNAPC3 and SNAPC4 occupy distinct positions in the SNAPc assembly that depend on SNAPC1 SUMOylation.\",\n      \"method\": \"Endogenous tagging, co-immunoprecipitation, CRISPR/dCas9-SENP1 targeting, inducible degron system\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with endogenous tags plus functional degron rescue system in single study\",\n      \"pmids\": [\"40956881\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SNAPC3 (SNAP43) is a core subunit of the five-subunit SNAPc complex that binds the PSE promoter element of snRNA genes and nucleates assembly of both RNA polymerase II and III transcription initiation complexes; it directly contacts TBP to facilitate TBP recruitment to the TATA box, engages in specific protein-protein interactions with SNAP50 and SNAP190 within the complex, and its assembly within SNAPc is regulated by SUMOylation of the SNAPC1 subunit, as revealed by biochemical reconstitution, cryo-EM structure, and endogenous-tagging experiments.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SNAPC3 (SNAP43) is a core subunit of the five-subunit small nuclear RNA-activating protein complex (SNAPc), which binds the proximal sequence element (PSE) of snRNA gene promoters and is essential for transcription initiation by both RNA polymerase II and RNA polymerase III [PMID:7715707, PMID:9732265]. Within SNAPc, SNAPC3 directly contacts SNAP50 and SNAP190 to form a minimal PSE-binding subcomplex, and it additionally interacts with the DNA-binding domain of TBP to recruit TBP to the TATA box of RNA polymerase III-dependent promoters such as U6 [PMID:11056176, PMID:12621023]. A 3.49 Å cryo-EM structure of the mini-SNAPc (SNAP190 N-terminus, SNAP50, and SNAPC3) bound to the U6-1 PSE reveals a wrap-around DNA-binding architecture in which SNAPC3 is an integral structural component [PMID:36369505]. SNAPC3 occupies a position in SNAPc assembly that is distinct from SNAPC4 (SNAP45) and is connected to SNAPC1 (SNAP19) through an interaction whose broader complex integrity is regulated by SNAPC1 SUMOylation [PMID:40956881].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Identification of SNAPC3 as a subunit of a novel TBP-TAF complex (SNAPc) that binds the PSE established the first molecular framework for how snRNA genes are transcribed by both RNA Pol II and Pol III.\",\n      \"evidence\": \"Biochemical purification and in vitro transcription assays from human cell extracts\",\n      \"pmids\": [\"7715707\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Individual contributions of each subunit to PSE binding were unknown\", \"No information on subunit–subunit contacts within the complex\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Mapping pairwise interactions showed SNAPC3 directly contacts SNAP50 but not SNAP45 or TBP, beginning to define the internal architecture of SNAPc.\",\n      \"evidence\": \"Co-immunoprecipitation and UV cross-linking in HeLa extracts\",\n      \"pmids\": [\"9003788\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Only pairwise interactions tested; higher-order contacts could be missed\", \"No domain-resolution mapping of the SNAPC3–SNAP50 interface\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Reconstitution of the complete five-subunit SNAPc from recombinant proteins demonstrated that SNAPC3 is essential for a functional complex capable of PSE binding and dual-polymerase transcription.\",\n      \"evidence\": \"Recombinant co-expression and in vitro transcription of both Pol II and Pol III snRNA templates\",\n      \"pmids\": [\"9732265\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure available to explain how five subunits cooperate for PSE recognition\", \"Mechanism by which SNAPc discriminates Pol II versus Pol III promoters remained unclear\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Systematic domain mapping identified specific regions of SNAPC3, SNAP50, and SNAP190 required for mutual association and PSE binding, showing the minimal determinants of complex assembly.\",\n      \"evidence\": \"Co-immunoprecipitation with deletion mutants and PSE EMSA\",\n      \"pmids\": [\"11056176\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution contacts between domains remained undetermined\", \"Functional contribution of individual domains to transcription not tested\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Discovery that a mini-SNAPc containing SNAPC3, SNAP50, and the SNAP190 N-terminus directly recruits TBP to the U6 TATA box resolved how SNAPc nucleates the Pol III preinitiation complex, with SNAPC3 making direct contact with TBP's DNA-binding domain.\",\n      \"evidence\": \"TBP recruitment assays, direct protein interaction mapping, and in vitro Pol III transcription with truncation mutants\",\n      \"pmids\": [\"12391172\", \"12621023\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the SNAPC3–TBP interaction unknown\", \"Whether SNAPC3–TBP contact is also relevant for Pol II snRNA transcription was not resolved\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Co-expression of a four-subunit partial SNAPc in E. coli confirmed that SNAPC3 is part of the minimal assembly sufficient for PSE binding, TBP recruitment, and both Pol II and Pol III transcription, validating the mini-SNAPc paradigm.\",\n      \"evidence\": \"Recombinant co-expression in E. coli with in vitro transcription of U1 and U6 templates\",\n      \"pmids\": [\"16603380\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Role of SNAP45 in the full complex assembly pathway remained structurally unresolved\", \"Post-translational regulation of the complex was unexplored\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A 3.49 Å cryo-EM structure of mini-SNAPc bound to U6-1 PSE revealed a wrap-around DNA-binding mode, providing the first atomic-level view of SNAPC3 within the complex and explaining how it contributes to the structural scaffold for PSE recognition.\",\n      \"evidence\": \"Cryo-EM structure determination of the human mini-SNAPc–PSE complex\",\n      \"pmids\": [\"36369505\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of full five-subunit SNAPc with SNAP19 and SNAP45 not determined\", \"SNAPC3–TBP interface not visualized structurally\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Endogenous tagging and deSUMOylation experiments showed that SNAPC3 and SNAPC4 occupy distinct assembly positions connected through SNAPC1, and that SNAPC1 SUMOylation regulates the SNAPC1–SNAPC4 but not the SNAPC1–SNAPC3 interaction, revealing a post-translational switch governing SNAPc integrity.\",\n      \"evidence\": \"Endogenous tagging, co-immunoprecipitation, CRISPR/dCas9-SENP1 targeting, and inducible degron system in human cells\",\n      \"pmids\": [\"40956881\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of disrupted SNAPC1–SNAPC4 interaction for snRNA transcription not directly measured\", \"Whether SUMOylation regulates SNAPc in different cell types or developmental contexts is unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of the SNAPC3–TBP interaction, the full five-subunit SNAPc structure including SNAP45 and SNAP19, and the mechanism by which SNAPc switches between Pol II and Pol III transcription modes remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of SNAPC3–TBP interface\", \"No complete five-subunit SNAPc structure\", \"Mechanism of Pol II versus Pol III promoter discrimination by SNAPc is not defined at the molecular level\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 2, 3, 7]},\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 2, 4, 6]}\n    ],\n    \"complexes\": [\n      \"SNAPc (snRNA-activating protein complex)\"\n    ],\n    \"partners\": [\n      \"SNAPC5\",\n      \"SNAPC4\",\n      \"SNAPC2\",\n      \"SNAPC1\",\n      \"TBP\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}