{"gene":"SF3A1","run_date":"2026-06-10T07:46:31","timeline":{"discoveries":[{"year":1993,"finding":"Yeast PRP21 (ortholog of SF3A1) is an integral component of the prespliceosome; anti-PRP21 antibodies co-immunoprecipitate U1 snRNA, U2 snRNA, and pre-mRNA in an ATP-dependent manner under splicing conditions, demonstrating stable association with U2 snRNP and/or pre-mRNA in the prespliceosomal complex.","method":"Co-immunoprecipitation with anti-PRP21 antibodies under splicing conditions; native gel analysis of splicing complexes","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal immunoprecipitation with functional (ATP-dependent, pre-mRNA-dependent) controls, replicated by complementary native gel analysis","pmids":["8341697"],"is_preprint":false},{"year":1993,"finding":"Yeast PRP21 (ortholog of SF3A1), together with PRP5, PRP9, and PRP11, is required for U2 snRNP binding to the pre-spliceosome during spliceosome assembly in vitro; genetic analyses suggest these proteins act concertedly and/or interact physically with each other and with stem-loop IIa of U2 snRNA.","method":"In vitro splicing assembly assays; genetic epistasis/complementation analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vitro functional assays combined with genetic epistasis, multiple orthogonal approaches","pmids":["8405998"],"is_preprint":false},{"year":1995,"finding":"Mammalian SF3A1 (SF3a120) contains tandem SURP modules in its N-terminal half and a C-terminal ubiquitin-like domain; binding studies with truncated derivatives showed that the SURP domains mediate binding to SF3a60 (SF3A2), whereas a 130-amino-acid region C-terminal to the SURP domains is essential for contacts with SF3a66 (SF3A3).","method":"Recombinant protein truncation/binding assays; cDNA cloning and domain mapping","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Moderate — systematic deletion mapping with multiple truncation constructs in binding assays, single lab but multiple orthogonal truncations tested","pmids":["7489498"],"is_preprint":false},{"year":1996,"finding":"Yeast Prp9, Prp11, and Prp21 form a direct protein complex (Prp9·Prp11·Prp21); purified recombinant proteins reconstituted this complex, which is functional in in vitro splicing. The complex also alters U2 snRNP structure, changing accessibility of the branch point pairing region of U2 snRNA to oligonucleotide-directed RNase H cleavage, suggesting a role in activating U2 snRNP for prespliceosome assembly.","method":"Recombinant protein purification (E. coli expression) and complex reconstitution; in vitro splicing assay; oligonucleotide-directed RNase H cleavage assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct in vitro reconstitution of complex from purified components, in vitro splicing rescue, and RNase H structural probing, single lab but multiple orthogonal methods","pmids":["8969185"],"is_preprint":false},{"year":1996,"finding":"In yeast, heat-sensitive prp21 point mutations cause defects in interaction with Prp9p but not with Prp11p, and most prp21 mutants show both a splicing defect and a pre-mRNA nuclear export phenotype; deletion analysis defined domains in Prp21p required for interactions with Prp9p and Prp11p, and these domains are conserved through evolution but do not include the SURP1 module.","method":"Yeast genetic analysis; heat-sensitive mutant isolation; protein-protein interaction assays; deletion analysis","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic genetic and domain deletion analysis in yeast, single lab, multiple mutant alleles tested","pmids":["8718683"],"is_preprint":false},{"year":2001,"finding":"Human SF3A1 (SF3a120) assembles the SF3a heterotrimer where SF3a60 and SF3a66 each interact with SF3A1 but not with each other; all three SF3a subunits are essential for formation of mature 17S U2 snRNP and the prespliceosome. SF3a60 plays a major role in recruiting SF3A1 into the U2 particle. C2H2-type zinc finger domains in SF3a60 and SF3a66 mediate their integration into the U2 snRNP, likely through protein-protein interactions with Sm proteins.","method":"Recombinant protein expression in insect cells; in vitro U2 snRNP and prespliceosome assembly assays; domain deletion and mutant analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstitution of U2 snRNP from recombinant subunits with multiple deletion constructs and functional assembly assays, single lab, multiple orthogonal methods","pmids":["11533230"],"is_preprint":false},{"year":2014,"finding":"SF3A1 protein of the U2 snRNP directly interacts with stem-loop 4 (SL4) of U1 snRNA; this interaction occurs within prespliceosomal complexes assembled on pre-mRNA, bridging the 5' and 3' splice site complexes. Free U1-SL4 added to a splicing reaction in vitro inhibits splicing and blocks assembly prior to the prespliceosomal A complex.","method":"SILAC; biotin/Neutravidin affinity pulldown; mass spectrometry; U1 snRNP complementation assay; in vitro splicing inhibition with free SL4","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — SILAC-MS identification confirmed by in vitro splicing inhibition and complex assembly assays, multiple orthogonal methods, functional consequence demonstrated","pmids":["25403181"],"is_preprint":false},{"year":2019,"finding":"The C-terminal ubiquitin-like (UBL) domain of SF3A1 functions as an RNA binding domain for U1-SL4; it binds U1-SL4 with high affinity (KD ~97 nM) as measured by EMSA and surface plasmon resonance. The double-stranded G-C rich stem of U1-SL4 is critical for UBL binding. Conserved tyrosines Y772 and Y773 are required for full binding affinity. SF3A1-UBL specifically pulls down U1 snRNP from HeLa nuclear extract.","method":"UV-crosslinking with deletion constructs; EMSA; surface plasmon resonance; site-directed mutagenesis; pulldown from HeLa nuclear extract","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — biochemical reconstitution with mutagenesis, binding constant determination by two orthogonal methods (EMSA and SPR), pulldown validation, single lab","pmids":["31383795"],"is_preprint":false},{"year":2022,"finding":"NMR solution structure of the SF3A1 SURP1 domain in complex with a fragment of splicing factor SF1 revealed that SURP1 adopts a canonical α1-α2-310-α3 topology; a hydrophobic patch on the SURP1 surface contacts a hydrophobic cluster on a 16-residue α-helix of SF1. Unlike SURP2 (which is permanently associated with SF3A3 via hydrophobic interactions only), SURP1-SF1 interactions also include salt bridges and hydrogen bonds. The SURP1-SF1 dissociation constant is ~20 μM, indicating a weak/transient interaction, consistent with SF1 dissociation during complex conversion.","method":"NMR structure determination; mutational analysis validated by bio-layer interferometry","journal":"Protein science : a publication of the Protein Society","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure with mutagenesis and binding affinity determination by bio-layer interferometry, single lab, multiple orthogonal methods","pmids":["36173164"],"is_preprint":false},{"year":2023,"finding":"Crystal structure (1.80 Å) of human SF3A1 ubiquitin-like domain (ULD, residues 704-785) complexed with U1 snRNA SL4 revealed a β-grasp fold; residues Lys756, Phe763, and Lys765 contact the UUCG tetraloop, while the C-terminal tail (786KERGGRKK793) contacts the major groove of the stem helix through main-chain and side-chain interactions. Putative post-translational modifications (e.g., ubiquitination) in ULD are predicted to directly inhibit SL4 binding. Mutational studies confirmed the binding interface.","method":"X-ray crystallography (1.80 Å); site-directed mutagenesis; bio-layer interferometry","journal":"Journal of biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution crystal structure with mutagenesis and binding quantification, single lab, multiple orthogonal methods","pmids":["37094335"],"is_preprint":false},{"year":1996,"finding":"Genetic analysis in yeast showed that a prp21 allele (prp21-2) suppresses the prp24-1 mutation and restores U6 snRNA levels, indicating a genetic interaction between PRP21 (SF3A1 ortholog, a U2 snRNP component) and PRP24 (a U6 snRNP component), providing evidence for functional U2-U6 snRNP interplay.","method":"Yeast genetic suppressor analysis; in vivo pre-mRNA splicing assay; allele-specificity tests","journal":"Molecular & general genetics : MGG","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic epistasis analysis showing allele-specific suppression, single lab, no direct biochemical validation","pmids":["8602141"],"is_preprint":false}],"current_model":"SF3A1 (SF3a120/SAP114/PRPF21/Prp21) is an essential U2 snRNP subunit that forms a heterotrimer with SF3A2 and SF3A3 via its SURP domains (binding SF3A2/SF3A3) and is required for assembly of the 17S U2 snRNP and prespliceosome; its SURP1 domain transiently contacts splicing factor SF1 to recruit U2 snRNP to early spliceosomal complexes, while its C-terminal ubiquitin-like domain binds stem-loop 4 of U1 snRNA (KD ~97 nM, mediated by Y772/Y773 and a C-terminal RGG tail) to bridge the 5' and 3' splice site complexes during prespliceosome assembly, with a 1.80 Å crystal structure defining the SL4 recognition interface."},"narrative":{"mechanistic_narrative":"SF3A1 (SF3a120/PRP21) is an essential subunit of the U2 snRNP that organizes the SF3a heterotrimer and drives recruitment of U2 snRNP into the prespliceosome during early spliceosome assembly [PMID:8341697, PMID:11533230]. As the scaffold of the SF3a complex, SF3A1 binds SF3A2 (SF3a60) through its tandem N-terminal SURP modules and SF3A3 (SF3a66) through a region C-terminal to the SURP domains, with all three subunits required to form mature 17S U2 snRNP and the prespliceosome [PMID:7489498, PMID:11533230]. The yeast ortholog assembles a functional Prp9·Prp11·Prp21 complex that alters U2 snRNA structure at the branch-point pairing region, indicating a role in activating U2 snRNP for prespliceosome assembly [PMID:8969185]. SF3A1 makes two distinct splice-site-bridging contacts: its SURP1 domain transiently engages a hydrophobic α-helix of splicing factor SF1 with weak affinity (KD ~20 μM), consistent with SF1 displacement during complex conversion [PMID:36173164], while its C-terminal ubiquitin-like domain binds stem-loop 4 of U1 snRNA with high affinity (KD ~97 nM) to bridge the 5' and 3' splice site complexes within prespliceosomal complexes [PMID:25403181, PMID:31383795]. Structural work resolves the UBL/ULD β-grasp fold contacting the U1-SL4 UUCG tetraloop and stem via tyrosines Y772/Y773, a C-terminal RGG/KERGGRKK tail, and residues Lys756/Phe763/Lys765, defining the SL4 recognition interface at 1.80 Å [PMID:31383795, PMID:37094335].","teleology":[{"year":1993,"claim":"Established that the SF3A1 ortholog is a stable, functional component of the assembled prespliceosome rather than a peripheral factor, and that its incorporation requires active spliceosome assembly.","evidence":"Co-immunoprecipitation with anti-PRP21 antibodies under splicing conditions and native gel analysis in yeast; in vitro assembly assays with genetic epistasis among PRP5/9/11/21","pmids":["8341697","8405998"],"confidence":"High","gaps":["Did not resolve which contacts are direct RNA vs protein","Mammalian counterpart not yet tested","Order of subunit recruitment unresolved"]},{"year":1996,"claim":"Showed that PRP21/SF3A1 nucleates a discrete trimeric complex with PRP9 and PRP11 that remodels U2 snRNA structure, linking SF3a assembly to functional activation of U2 snRNP.","evidence":"Recombinant reconstitution from purified yeast proteins, in vitro splicing rescue, RNase H structural probing; heat-sensitive prp21 allele and deletion mapping of Prp9/Prp11 interaction domains","pmids":["8969185","8718683"],"confidence":"High","gaps":["Mechanism of how U2 branch-point region is remodeled unresolved","SURP1 role not addressed by these interactions","Export phenotype mechanism unexplained"]},{"year":1996,"claim":"Genetic suppression linked PRP21 to U6 snRNP function, hinting at U2–U6 interplay coordinated through this U2 subunit.","evidence":"Yeast suppressor analysis showing prp21-2 suppresses prp24-1 and restores U6 levels, with allele-specificity tests","pmids":["8602141"],"confidence":"Medium","gaps":["Genetic interaction only, no direct biochemical validation","Physical basis of U2-U6 link not established","Relevance to human SF3A1 untested"]},{"year":2001,"claim":"Defined the architecture of the human SF3a heterotrimer, placing SF3A1 as the central scaffold bound independently by SF3A2 and SF3A3, all required for 17S U2 snRNP and prespliceosome formation.","evidence":"Recombinant expression in insect cells with in vitro U2 snRNP/prespliceosome assembly and domain deletion mutants","pmids":["11533230"],"confidence":"High","gaps":["Did not address SF3A1 contacts to other snRNPs","Stoichiometry within U2 not fully resolved","Dynamics of assembly not captured"]},{"year":2014,"claim":"Identified a direct SF3A1–U1-SL4 contact that bridges the 5' and 3' splice-site complexes, revealing how a U2 subunit physically couples the two ends of an intron during prespliceosome formation.","evidence":"SILAC affinity pulldown and mass spectrometry, U1 snRNP complementation, and in vitro splicing inhibition with free SL4","pmids":["25403181"],"confidence":"High","gaps":["Which SF3A1 domain mediates SL4 binding not yet mapped","Structural basis of recognition unknown","In vivo requirement not directly tested"]},{"year":2019,"claim":"Mapped the U1-SL4 binding activity to the SF3A1 C-terminal ubiquitin-like domain and quantified a high-affinity, sequence/structure-specific interaction.","evidence":"UV-crosslinking with deletion constructs, EMSA, surface plasmon resonance, site-directed mutagenesis of Y772/Y773, and pulldown from HeLa nuclear extract","pmids":["31383795"],"confidence":"High","gaps":["Atomic-resolution interface not yet defined","Regulation of the interaction unknown","Effect of UBL mutations in cells untested"]},{"year":2022,"claim":"Solved the SURP1–SF1 interface, explaining how SF3A1 transiently recruits U2 snRNP via SF1 and why this contact is weak enough to permit SF1 displacement during complex conversion.","evidence":"NMR solution structure of SURP1–SF1 fragment complex with mutagenesis validated by bio-layer interferometry (KD ~20 μM)","pmids":["36173164"],"confidence":"High","gaps":["Timing of SF1 release in the full assembly pathway not resolved","Functional consequence of disrupting SURP1-SF1 in cells untested","Coordination with UBL-SL4 binding unknown"]},{"year":2023,"claim":"Provided a high-resolution view of the UBL/ULD–U1-SL4 complex, defining the precise residues recognizing the tetraloop and stem and predicting how post-translational modification could regulate the bridging interaction.","evidence":"1.80 Å crystal structure of SF3A1 ULD (704-785) with U1-SL4, site-directed mutagenesis, and bio-layer interferometry","pmids":["37094335"],"confidence":"High","gaps":["Predicted regulatory ubiquitination not experimentally confirmed","Structure of full SF3A1 within U2 snRNP context lacking","Dynamics of bridge formation/release not captured"]},{"year":null,"claim":"How SF3A1's two bridging activities (SURP1–SF1 and UBL–U1-SL4) are temporally coordinated and regulated during the transition from prespliceosome to activated spliceosome remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No integrated model of SF1 release relative to U1-SL4 engagement","Regulatory PTMs on the ULD not demonstrated in vivo","No structure of SF3A1 in the full assembled prespliceosome"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[6,7,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,5,6]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[3,5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,5,6]}],"complexes":["SF3a heterotrimer","17S U2 snRNP","prespliceosome","Prp9·Prp11·Prp21 complex"],"partners":["SF3A2","SF3A3","SF1","PRP9","PRP11"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q15459","full_name":"Splicing factor 3A subunit 1","aliases":["SF3a120","Spliceosome-associated protein 114","SAP 114"],"length_aa":793,"mass_kda":88.9,"function":"Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:10882114, PubMed:11533230, PubMed:32494006). The 17S U2 SnRNP complex (1) directly participates in early spliceosome assembly and (2) mediates recognition of the intron branch site during pre-mRNA splicing by promoting the selection of the pre-mRNA branch-site adenosine, the nucleophile for the first step of splicing (PubMed:10882114, PubMed:11533230, PubMed:32494006). Within the 17S U2 SnRNP complex, SF3A1 is part of the SF3A subcomplex that contributes to the assembly of the 17S U2 snRNP, and the subsequent assembly of the pre-spliceosome 'E' complex and the pre-catalytic spliceosome 'A' complex (PubMed:10882114, PubMed:11533230). Involved in pre-mRNA splicing as a component of pre-catalytic spliceosome 'B' complexes (PubMed:29360106, PubMed:30315277)","subcellular_location":"Nucleus; Nucleus speckle","url":"https://www.uniprot.org/uniprotkb/Q15459/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SF3A1","classification":"Common Essential","n_dependent_lines":1206,"n_total_lines":1208,"dependency_fraction":0.9983443708609272},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000099995","cell_line_id":"CID001444","localizations":[{"compartment":"chromatin","grade":3}],"interactors":[{"gene":"RBM17","stoichiometry":10.0},{"gene":"SNRPD2","stoichiometry":10.0},{"gene":"SF3B3","stoichiometry":10.0},{"gene":"SF3B4","stoichiometry":10.0},{"gene":"SF3A3","stoichiometry":10.0},{"gene":"SF3B2","stoichiometry":10.0},{"gene":"SF3B6","stoichiometry":10.0},{"gene":"SF3B5","stoichiometry":10.0},{"gene":"SNRPA1","stoichiometry":10.0},{"gene":"U2SURP","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID001444","total_profiled":1310},"omim":[{"mim_id":"605596","title":"SPLICING FACTOR 3A, SUBUNIT 3; SF3A3","url":"https://www.omim.org/entry/605596"},{"mim_id":"605595","title":"SPLICING FACTOR 3A, SUBUNIT 1; SF3A1","url":"https://www.omim.org/entry/605595"},{"mim_id":"605590","title":"SPLICING FACTOR 3B, SUBUNIT 1; SF3B1","url":"https://www.omim.org/entry/605590"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Nuclear speckles","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SF3A1"},"hgnc":{"alias_symbol":["SF3a120","SAP114","PRPF21","Prp21"],"prev_symbol":[]},"alphafold":{"accession":"Q15459","domains":[{"cath_id":"1.10.10.790","chopping":"46-102","consensus_level":"high","plddt":86.1923,"start":46,"end":102},{"cath_id":"1.10.10.790","chopping":"160-251","consensus_level":"medium","plddt":88.989,"start":160,"end":251},{"cath_id":"3.10.20.90","chopping":"693-784","consensus_level":"high","plddt":89.5816,"start":693,"end":784}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15459","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q15459-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q15459-F1-predicted_aligned_error_v6.png","plddt_mean":66.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SF3A1","jax_strain_url":"https://www.jax.org/strain/search?query=SF3A1"},"sequence":{"accession":"Q15459","fasta_url":"https://rest.uniprot.org/uniprotkb/Q15459.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q15459/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15459"}},"corpus_meta":[{"pmid":"8405998","id":"PMC_8405998","title":"Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA.","date":"1993","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/8405998","citation_count":125,"is_preprint":false},{"pmid":"25403181","id":"PMC_25403181","title":"Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly.","date":"2014","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/25403181","citation_count":56,"is_preprint":false},{"pmid":"7489498","id":"PMC_7489498","title":"Mammalian splicing factor SF3a120 represents a new member of the SURP family of proteins and is homologous to the essential splicing factor PRP21p of Saccharomyces cerevisiae.","date":"1995","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/7489498","citation_count":56,"is_preprint":false},{"pmid":"11533230","id":"PMC_11533230","title":"Domains in human splicing factors SF3a60 and SF3a66 required for binding to SF3a120, assembly of the 17S U2 snRNP, and prespliceosome formation.","date":"2001","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11533230","citation_count":49,"is_preprint":false},{"pmid":"8341697","id":"PMC_8341697","title":"The Saccharomyces cerevisiae PRP21 gene product is an integral component of the prespliceosome.","date":"1993","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/8341697","citation_count":43,"is_preprint":false},{"pmid":"8969185","id":"PMC_8969185","title":"In vitro studies of the Prp9.Prp11.Prp21 complex indicate a pathway for U2 small nuclear ribonucleoprotein activation.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8969185","citation_count":36,"is_preprint":false},{"pmid":"7971282","id":"PMC_7971282","title":"SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins.","date":"1994","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/7971282","citation_count":27,"is_preprint":false},{"pmid":"31383795","id":"PMC_31383795","title":"Identification of a noncanonical RNA binding domain in the U2 snRNP protein SF3A1.","date":"2019","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/31383795","citation_count":21,"is_preprint":false},{"pmid":"26498691","id":"PMC_26498691","title":"SF3A1 and pancreatic cancer: new evidence for the association of the spliceosome and cancer.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26498691","citation_count":19,"is_preprint":false},{"pmid":"7754713","id":"PMC_7754713","title":"The sequence of a 36 kb segment on the left arm of yeast chromosome X identifies 24 open reading frames including NUC1, PRP21 (SPP91), CDC6, CRY2, the gene for S24, a homologue to the aconitase gene ACO1 and two homologues to chromosome III genes.","date":"1994","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/7754713","citation_count":16,"is_preprint":false},{"pmid":"36173164","id":"PMC_36173164","title":"Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1.","date":"2022","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/36173164","citation_count":13,"is_preprint":false},{"pmid":"8718683","id":"PMC_8718683","title":"Essential domains of the PRP21 splicing factor are implicated in the binding to PRP9 and PRP11 proteins and are conserved through evolution.","date":"1996","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8718683","citation_count":13,"is_preprint":false},{"pmid":"26079486","id":"PMC_26079486","title":"The Associations between RNA Splicing Complex Gene SF3A1 Polymorphisms and Colorectal Cancer Risk in a Chinese Population.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26079486","citation_count":8,"is_preprint":false},{"pmid":"10545445","id":"PMC_10545445","title":"A mutation in a methionine tRNA gene suppresses the prp2-1 Ts mutation and causes a pre-mRNA splicing defect in Saccharomyces cerevisiae.","date":"1999","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/10545445","citation_count":6,"is_preprint":false},{"pmid":"8602141","id":"PMC_8602141","title":"An extragenic suppressor of prp24-1 defines genetic interaction between PRP24 and PRP21 gene products of Saccharomyces cerevisiae.","date":"1996","source":"Molecular & general genetics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/8602141","citation_count":4,"is_preprint":false},{"pmid":"37094335","id":"PMC_37094335","title":"Structural insights into recognition of SL4, the UUCG stem-loop, of human U1 snRNA by the ubiquitin-like domain, including the C-terminal tail in the SF3A1 subunit of U2 snRNP.","date":"2023","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37094335","citation_count":2,"is_preprint":false},{"pmid":"40302801","id":"PMC_40302801","title":"SF3a1: A Novel Potential Tumor Biomarker or Therapeutic Target.","date":"2025","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40302801","citation_count":1,"is_preprint":false},{"pmid":"40449648","id":"PMC_40449648","title":"Hydroxysafflor yellow A alleviates ischemic myocardial injury by targeting SF3A1 to improve mitochondrial energy metabolism.","date":"2025","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40449648","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10623,"output_tokens":3219,"usd":0.040077,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10596,"output_tokens":3186,"usd":0.066315,"stage2_stop_reason":"end_turn"},"total_usd":0.106392,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1993,\n      \"finding\": \"Yeast PRP21 (ortholog of SF3A1) is an integral component of the prespliceosome; anti-PRP21 antibodies co-immunoprecipitate U1 snRNA, U2 snRNA, and pre-mRNA in an ATP-dependent manner under splicing conditions, demonstrating stable association with U2 snRNP and/or pre-mRNA in the prespliceosomal complex.\",\n      \"method\": \"Co-immunoprecipitation with anti-PRP21 antibodies under splicing conditions; native gel analysis of splicing complexes\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal immunoprecipitation with functional (ATP-dependent, pre-mRNA-dependent) controls, replicated by complementary native gel analysis\",\n      \"pmids\": [\"8341697\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Yeast PRP21 (ortholog of SF3A1), together with PRP5, PRP9, and PRP11, is required for U2 snRNP binding to the pre-spliceosome during spliceosome assembly in vitro; genetic analyses suggest these proteins act concertedly and/or interact physically with each other and with stem-loop IIa of U2 snRNA.\",\n      \"method\": \"In vitro splicing assembly assays; genetic epistasis/complementation analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vitro functional assays combined with genetic epistasis, multiple orthogonal approaches\",\n      \"pmids\": [\"8405998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Mammalian SF3A1 (SF3a120) contains tandem SURP modules in its N-terminal half and a C-terminal ubiquitin-like domain; binding studies with truncated derivatives showed that the SURP domains mediate binding to SF3a60 (SF3A2), whereas a 130-amino-acid region C-terminal to the SURP domains is essential for contacts with SF3a66 (SF3A3).\",\n      \"method\": \"Recombinant protein truncation/binding assays; cDNA cloning and domain mapping\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic deletion mapping with multiple truncation constructs in binding assays, single lab but multiple orthogonal truncations tested\",\n      \"pmids\": [\"7489498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Yeast Prp9, Prp11, and Prp21 form a direct protein complex (Prp9·Prp11·Prp21); purified recombinant proteins reconstituted this complex, which is functional in in vitro splicing. The complex also alters U2 snRNP structure, changing accessibility of the branch point pairing region of U2 snRNA to oligonucleotide-directed RNase H cleavage, suggesting a role in activating U2 snRNP for prespliceosome assembly.\",\n      \"method\": \"Recombinant protein purification (E. coli expression) and complex reconstitution; in vitro splicing assay; oligonucleotide-directed RNase H cleavage assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct in vitro reconstitution of complex from purified components, in vitro splicing rescue, and RNase H structural probing, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"8969185\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"In yeast, heat-sensitive prp21 point mutations cause defects in interaction with Prp9p but not with Prp11p, and most prp21 mutants show both a splicing defect and a pre-mRNA nuclear export phenotype; deletion analysis defined domains in Prp21p required for interactions with Prp9p and Prp11p, and these domains are conserved through evolution but do not include the SURP1 module.\",\n      \"method\": \"Yeast genetic analysis; heat-sensitive mutant isolation; protein-protein interaction assays; deletion analysis\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic genetic and domain deletion analysis in yeast, single lab, multiple mutant alleles tested\",\n      \"pmids\": [\"8718683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Human SF3A1 (SF3a120) assembles the SF3a heterotrimer where SF3a60 and SF3a66 each interact with SF3A1 but not with each other; all three SF3a subunits are essential for formation of mature 17S U2 snRNP and the prespliceosome. SF3a60 plays a major role in recruiting SF3A1 into the U2 particle. C2H2-type zinc finger domains in SF3a60 and SF3a66 mediate their integration into the U2 snRNP, likely through protein-protein interactions with Sm proteins.\",\n      \"method\": \"Recombinant protein expression in insect cells; in vitro U2 snRNP and prespliceosome assembly assays; domain deletion and mutant analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstitution of U2 snRNP from recombinant subunits with multiple deletion constructs and functional assembly assays, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"11533230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SF3A1 protein of the U2 snRNP directly interacts with stem-loop 4 (SL4) of U1 snRNA; this interaction occurs within prespliceosomal complexes assembled on pre-mRNA, bridging the 5' and 3' splice site complexes. Free U1-SL4 added to a splicing reaction in vitro inhibits splicing and blocks assembly prior to the prespliceosomal A complex.\",\n      \"method\": \"SILAC; biotin/Neutravidin affinity pulldown; mass spectrometry; U1 snRNP complementation assay; in vitro splicing inhibition with free SL4\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — SILAC-MS identification confirmed by in vitro splicing inhibition and complex assembly assays, multiple orthogonal methods, functional consequence demonstrated\",\n      \"pmids\": [\"25403181\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The C-terminal ubiquitin-like (UBL) domain of SF3A1 functions as an RNA binding domain for U1-SL4; it binds U1-SL4 with high affinity (KD ~97 nM) as measured by EMSA and surface plasmon resonance. The double-stranded G-C rich stem of U1-SL4 is critical for UBL binding. Conserved tyrosines Y772 and Y773 are required for full binding affinity. SF3A1-UBL specifically pulls down U1 snRNP from HeLa nuclear extract.\",\n      \"method\": \"UV-crosslinking with deletion constructs; EMSA; surface plasmon resonance; site-directed mutagenesis; pulldown from HeLa nuclear extract\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — biochemical reconstitution with mutagenesis, binding constant determination by two orthogonal methods (EMSA and SPR), pulldown validation, single lab\",\n      \"pmids\": [\"31383795\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NMR solution structure of the SF3A1 SURP1 domain in complex with a fragment of splicing factor SF1 revealed that SURP1 adopts a canonical α1-α2-310-α3 topology; a hydrophobic patch on the SURP1 surface contacts a hydrophobic cluster on a 16-residue α-helix of SF1. Unlike SURP2 (which is permanently associated with SF3A3 via hydrophobic interactions only), SURP1-SF1 interactions also include salt bridges and hydrogen bonds. The SURP1-SF1 dissociation constant is ~20 μM, indicating a weak/transient interaction, consistent with SF1 dissociation during complex conversion.\",\n      \"method\": \"NMR structure determination; mutational analysis validated by bio-layer interferometry\",\n      \"journal\": \"Protein science : a publication of the Protein Society\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure with mutagenesis and binding affinity determination by bio-layer interferometry, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"36173164\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Crystal structure (1.80 Å) of human SF3A1 ubiquitin-like domain (ULD, residues 704-785) complexed with U1 snRNA SL4 revealed a β-grasp fold; residues Lys756, Phe763, and Lys765 contact the UUCG tetraloop, while the C-terminal tail (786KERGGRKK793) contacts the major groove of the stem helix through main-chain and side-chain interactions. Putative post-translational modifications (e.g., ubiquitination) in ULD are predicted to directly inhibit SL4 binding. Mutational studies confirmed the binding interface.\",\n      \"method\": \"X-ray crystallography (1.80 Å); site-directed mutagenesis; bio-layer interferometry\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution crystal structure with mutagenesis and binding quantification, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37094335\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Genetic analysis in yeast showed that a prp21 allele (prp21-2) suppresses the prp24-1 mutation and restores U6 snRNA levels, indicating a genetic interaction between PRP21 (SF3A1 ortholog, a U2 snRNP component) and PRP24 (a U6 snRNP component), providing evidence for functional U2-U6 snRNP interplay.\",\n      \"method\": \"Yeast genetic suppressor analysis; in vivo pre-mRNA splicing assay; allele-specificity tests\",\n      \"journal\": \"Molecular & general genetics : MGG\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis analysis showing allele-specific suppression, single lab, no direct biochemical validation\",\n      \"pmids\": [\"8602141\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SF3A1 (SF3a120/SAP114/PRPF21/Prp21) is an essential U2 snRNP subunit that forms a heterotrimer with SF3A2 and SF3A3 via its SURP domains (binding SF3A2/SF3A3) and is required for assembly of the 17S U2 snRNP and prespliceosome; its SURP1 domain transiently contacts splicing factor SF1 to recruit U2 snRNP to early spliceosomal complexes, while its C-terminal ubiquitin-like domain binds stem-loop 4 of U1 snRNA (KD ~97 nM, mediated by Y772/Y773 and a C-terminal RGG tail) to bridge the 5' and 3' splice site complexes during prespliceosome assembly, with a 1.80 Å crystal structure defining the SL4 recognition interface.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SF3A1 (SF3a120/PRP21) is an essential subunit of the U2 snRNP that organizes the SF3a heterotrimer and drives recruitment of U2 snRNP into the prespliceosome during early spliceosome assembly [#0, #5]. As the scaffold of the SF3a complex, SF3A1 binds SF3A2 (SF3a60) through its tandem N-terminal SURP modules and SF3A3 (SF3a66) through a region C-terminal to the SURP domains, with all three subunits required to form mature 17S U2 snRNP and the prespliceosome [#2, #5]. The yeast ortholog assembles a functional Prp9·Prp11·Prp21 complex that alters U2 snRNA structure at the branch-point pairing region, indicating a role in activating U2 snRNP for prespliceosome assembly [#3]. SF3A1 makes two distinct splice-site-bridging contacts: its SURP1 domain transiently engages a hydrophobic α-helix of splicing factor SF1 with weak affinity (KD ~20 μM), consistent with SF1 displacement during complex conversion [#8], while its C-terminal ubiquitin-like domain binds stem-loop 4 of U1 snRNA with high affinity (KD ~97 nM) to bridge the 5' and 3' splice site complexes within prespliceosomal complexes [#6, #7]. Structural work resolves the UBL/ULD β-grasp fold contacting the U1-SL4 UUCG tetraloop and stem via tyrosines Y772/Y773, a C-terminal RGG/KERGGRKK tail, and residues Lys756/Phe763/Lys765, defining the SL4 recognition interface at 1.80 Å [#7, #9].\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established that the SF3A1 ortholog is a stable, functional component of the assembled prespliceosome rather than a peripheral factor, and that its incorporation requires active spliceosome assembly.\",\n      \"evidence\": \"Co-immunoprecipitation with anti-PRP21 antibodies under splicing conditions and native gel analysis in yeast; in vitro assembly assays with genetic epistasis among PRP5/9/11/21\",\n      \"pmids\": [\"8341697\", \"8405998\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which contacts are direct RNA vs protein\", \"Mammalian counterpart not yet tested\", \"Order of subunit recruitment unresolved\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Showed that PRP21/SF3A1 nucleates a discrete trimeric complex with PRP9 and PRP11 that remodels U2 snRNA structure, linking SF3a assembly to functional activation of U2 snRNP.\",\n      \"evidence\": \"Recombinant reconstitution from purified yeast proteins, in vitro splicing rescue, RNase H structural probing; heat-sensitive prp21 allele and deletion mapping of Prp9/Prp11 interaction domains\",\n      \"pmids\": [\"8969185\", \"8718683\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of how U2 branch-point region is remodeled unresolved\", \"SURP1 role not addressed by these interactions\", \"Export phenotype mechanism unexplained\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Genetic suppression linked PRP21 to U6 snRNP function, hinting at U2–U6 interplay coordinated through this U2 subunit.\",\n      \"evidence\": \"Yeast suppressor analysis showing prp21-2 suppresses prp24-1 and restores U6 levels, with allele-specificity tests\",\n      \"pmids\": [\"8602141\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Genetic interaction only, no direct biochemical validation\", \"Physical basis of U2-U6 link not established\", \"Relevance to human SF3A1 untested\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defined the architecture of the human SF3a heterotrimer, placing SF3A1 as the central scaffold bound independently by SF3A2 and SF3A3, all required for 17S U2 snRNP and prespliceosome formation.\",\n      \"evidence\": \"Recombinant expression in insect cells with in vitro U2 snRNP/prespliceosome assembly and domain deletion mutants\",\n      \"pmids\": [\"11533230\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address SF3A1 contacts to other snRNPs\", \"Stoichiometry within U2 not fully resolved\", \"Dynamics of assembly not captured\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified a direct SF3A1–U1-SL4 contact that bridges the 5' and 3' splice-site complexes, revealing how a U2 subunit physically couples the two ends of an intron during prespliceosome formation.\",\n      \"evidence\": \"SILAC affinity pulldown and mass spectrometry, U1 snRNP complementation, and in vitro splicing inhibition with free SL4\",\n      \"pmids\": [\"25403181\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which SF3A1 domain mediates SL4 binding not yet mapped\", \"Structural basis of recognition unknown\", \"In vivo requirement not directly tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Mapped the U1-SL4 binding activity to the SF3A1 C-terminal ubiquitin-like domain and quantified a high-affinity, sequence/structure-specific interaction.\",\n      \"evidence\": \"UV-crosslinking with deletion constructs, EMSA, surface plasmon resonance, site-directed mutagenesis of Y772/Y773, and pulldown from HeLa nuclear extract\",\n      \"pmids\": [\"31383795\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution interface not yet defined\", \"Regulation of the interaction unknown\", \"Effect of UBL mutations in cells untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Solved the SURP1–SF1 interface, explaining how SF3A1 transiently recruits U2 snRNP via SF1 and why this contact is weak enough to permit SF1 displacement during complex conversion.\",\n      \"evidence\": \"NMR solution structure of SURP1–SF1 fragment complex with mutagenesis validated by bio-layer interferometry (KD ~20 μM)\",\n      \"pmids\": [\"36173164\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Timing of SF1 release in the full assembly pathway not resolved\", \"Functional consequence of disrupting SURP1-SF1 in cells untested\", \"Coordination with UBL-SL4 binding unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided a high-resolution view of the UBL/ULD–U1-SL4 complex, defining the precise residues recognizing the tetraloop and stem and predicting how post-translational modification could regulate the bridging interaction.\",\n      \"evidence\": \"1.80 Å crystal structure of SF3A1 ULD (704-785) with U1-SL4, site-directed mutagenesis, and bio-layer interferometry\",\n      \"pmids\": [\"37094335\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Predicted regulatory ubiquitination not experimentally confirmed\", \"Structure of full SF3A1 within U2 snRNP context lacking\", \"Dynamics of bridge formation/release not captured\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SF3A1's two bridging activities (SURP1–SF1 and UBL–U1-SL4) are temporally coordinated and regulated during the transition from prespliceosome to activated spliceosome remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No integrated model of SF1 release relative to U1-SL4 engagement\", \"Regulatory PTMs on the ULD not demonstrated in vivo\", \"No structure of SF3A1 in the full assembled prespliceosome\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [6, 7, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 5, 6]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 5, 6]}\n    ],\n    \"complexes\": [\"SF3a heterotrimer\", \"17S U2 snRNP\", \"prespliceosome\", \"Prp9·Prp11·Prp21 complex\"],\n    \"partners\": [\"SF3A2\", \"SF3A3\", \"SF1\", \"PRP9\", \"PRP11\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}