Affinage

SF3A1

Splicing factor 3A subunit 1 · UniProt Q15459

Round 2 corrected
Length
793 aa
Mass
88.9 kDa
Annotated
2026-04-28
48 papers in source corpus 14 papers cited in narrative 14 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SF3A1 is a core subunit of the SF3a heterotrimer (with SF3A2/SF3A60 and SF3A3/SF3A66) within the 17S U2 snRNP, essential for prespliceosome assembly and pre-mRNA splicing. Its N-terminal tandem SURP domains mediate distinct protein–protein interactions: SURP1 transiently recruits U2 snRNP to early spliceosomal complexes via a low-affinity contact with splicing factor SF1, while SURP2 stably associates with SF3A3 (PMID:36173164, PMID:7489498). The C-terminal ubiquitin-like domain (ULD) functions as a noncanonical RNA-binding module that directly contacts stem-loop 4 of U1 snRNA with nanomolar affinity, bridging the 5′ and 3′ splice-site complexes during A-complex formation and thereby coupling splice-site recognition across the intron (PMID:25403181, PMID:31383795, PMID:37094335). Reconstitution of the yeast SF3a trimer (Prp9·Prp11·Prp21) demonstrated that the complex restructures U2 snRNP to increase accessibility of the branch-point interaction region of U2 snRNA (PMID:8969185).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1993 High

    Establishing that PRP21/SF3A1 is an integral U2 snRNP component required for prespliceosome assembly resolved how U2 snRNP engages pre-mRNA in an ATP-dependent manner.

    Evidence Co-immunoprecipitation with anti-PRP21 antibodies and native gel splicing complex analysis in yeast extracts; parallel genetic and biochemical complementation studies

    PMID:8341697 PMID:8405998

    Open questions at the time
    • No direct structural information on PRP21 domains
    • Mechanism by which the SF3a complex activates U2 snRNP unknown
    • Mammalian homolog not yet characterized
  2. 1995 High

    Identification of mammalian SF3A1 (SF3A120) as the PRP21 homolog and mapping of its domain architecture — tandem SURP modules for SF3A60/SF3A66 binding and a C-terminal ubiquitin-like domain — established the modular organization that organizes the SF3a heterotrimer.

    Evidence cDNA cloning and binding assays with truncated SF3A120 derivatives

    PMID:7489498

    Open questions at the time
    • Binding partners of the SURP1 module beyond SF3A60 not identified
    • Function of the ubiquitin-like domain unknown
    • Atomic-resolution structural data lacking
  3. 1996 High

    Reconstitution of the yeast trimeric SF3a complex (Prp9·Prp11·Prp21) from recombinant proteins showed it restructures U2 snRNP to expose the branch-point interaction region, explaining how SF3a activates U2 for pre-mRNA binding.

    Evidence E. coli-expressed trimer; in vitro splicing assay; oligonucleotide-directed RNase H accessibility probing

    PMID:8969185

    Open questions at the time
    • Precise RNA contacts made by the trimer not mapped
    • Structural basis of U2 snRNA remodeling unknown
  4. 1996 High

    Mutagenesis of PRP21 revealed that its central domains mediate the essential interaction with Prp9p, while the most conserved SURP1 module is dispensable for viability under standard conditions, posing the question of what additional function SURP1 serves.

    Evidence Temperature-sensitive point mutations and domain deletions with in vivo splicing assays in yeast

    PMID:8718683

    Open questions at the time
    • SURP1 binding partner in metazoans not identified
    • The genetic interaction between PRP21 and U6 snRNP factor PRP24 (PMID:8602141) lacks a biochemical mechanism
  5. 2001 High

    Systematic reconstitution of 17S U2 snRNP assembly showed that all three SF3a subunits are essential for the mature particle and that SF3A60 and SF3A66 each contact SF3A1 but not each other, establishing the hub architecture of SF3A1 within the trimer.

    Evidence Insect-cell co-expression; in vitro 17S U2 snRNP and prespliceosome assembly assays with domain deletions

    PMID:11533230

    Open questions at the time
    • No high-resolution structure of the intact SF3a trimer
    • Integration contacts between SF3a and the rest of 17S U2 snRNP not mapped at residue level
  6. 2014 High

    Discovery that SF3A1, a U2 snRNP protein, directly contacts stem-loop 4 of U1 snRNA during prespliceosome assembly revealed an unexpected cross-snRNP bridge that physically connects the 5′ and 3′ splice-site complexes and is required for A-complex formation.

    Evidence SILAC quantitative mass spectrometry; biotin-SL4 pull-down; competition with free SL4 RNA blocks splicing and A-complex formation in vitro

    PMID:25403181

    Open questions at the time
    • Which domain of SF3A1 mediates the U1-SL4 contact not yet determined
    • Structural basis of the interaction unknown
  7. 2019 High

    Identification of the SF3A1 C-terminal ubiquitin-like domain as the noncanonical RNA-binding module responsible for high-affinity U1-SL4 recognition resolved which domain bridges U1 and U2 snRNPs and assigned a molecular function to the previously enigmatic UBL domain.

    Evidence UV-crosslinking with deletion constructs; EMSA; SPR (KD ~97 nM); Y772/Y773 mutagenesis; UBL pull-down of intact U1 snRNP from HeLa extract

    PMID:31383795

    Open questions at the time
    • Atomic-resolution structure of the UBL–SL4 complex not available
    • Regulatory role of post-translational modifications on the UBL not tested
  8. 2022 High

    NMR structure of the SF3A1 SURP1 domain bound to an SF1 helix answered the long-standing question of SURP1 function: it transiently recruits SF1-marked branch-point complexes to U2 snRNP, while SURP2 permanently engages SF3A3.

    Evidence NMR solution structure; bio-layer interferometry (KD ~20 µM); mutagenesis of hydrophobic patch

    PMID:36173164

    Open questions at the time
    • Functional consequence of disrupting the SURP1–SF1 interaction in vivo not tested
    • Whether SURP1 has additional interaction partners beyond SF1 remains open
  9. 2023 High

    The 1.80 Å crystal structure of the SF3A1 ULD–U1 SL4 complex provided an atomic mechanism for cross-snRNP bridging: the β-grasp fold contacts the UUCG tetraloop via three ULD-specific residues while the C-terminal RGG-containing tail engages the major groove of the SL4 stem, and the structure predicted that ubiquitination within the ULD would directly block RNA binding.

    Evidence X-ray crystallography; bio-layer interferometry; mutagenesis of key contact residues

    PMID:37094335

    Open questions at the time
    • Ubiquitination-mediated regulation of ULD–SL4 binding not demonstrated in cells
    • Structural context of ULD–SL4 within the intact prespliceosome not resolved
  10. 2025 Medium

    SF3A1 knockdown impairs mitochondrial energy metabolism and abolishes protective effects against myocardial ischemia/reperfusion injury, extending SF3A1's functional impact beyond canonical splicing to metabolic fitness in cardiomyocytes.

    Evidence Thermal proteome profiling for target identification; siRNA knockdown; mitochondrial function assays and in vivo mouse MI model

    PMID:40449648

    Open questions at the time
    • Whether the metabolic phenotype is a direct or indirect consequence of splicing perturbation is unresolved
    • Specific splice targets mediating the mitochondrial phenotype not identified
    • Single-lab finding requiring independent replication

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include whether post-translational ubiquitination of the ULD regulates SL4 binding in vivo to modulate splice-site pairing, and how the full SF3a–U2 snRNP–U1 snRNP bridging architecture is organized within the intact prespliceosome.
  • No in vivo demonstration that ULD ubiquitination regulates splicing
  • No cryo-EM or crystal structure of SF3A1 in the context of a complete prespliceosomal complex
  • Functional role of the SF3A1 proline-rich region remains uncharacterized

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0005198 structural molecule activity 3 GO:0060090 molecular adaptor activity 2
Localization
GO:0005634 nucleus 3 GO:0005654 nucleoplasm 2
Pathway
R-HSA-8953854 Metabolism of RNA 6
Partners
NCBP1SF1SF3A2SF3A3
Complex memberships
17S U2 snRNPSF3a heterotrimer

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1993 PRP21 (the yeast ortholog of SF3A1) is an integral component of the prespliceosome, stably associated with U2 snRNP and pre-mRNA. Anti-PRP21 antibodies co-immunoprecipitate U1 snRNA, U2 snRNA, and pre-mRNA in an ATP-dependent manner, and prespliceosomes are specifically pulled down, demonstrating PRP21's role in prespliceosome assembly. Co-immunoprecipitation with anti-PRP21 antibodies under various salt conditions; native gel analysis of splicing complexes; in vitro splicing assay Proceedings of the National Academy of Sciences of the United States of America High 8341697
1993 PRP5, PRP9, PRP11, and PRP21 (the latter being the yeast ortholog of SF3A1) are each required for U2 snRNP binding to the pre-spliceosome during spliceosome assembly in vitro. PRP9 and PRP11 interact physically with each other, and genetic analyses suggest all four act concertedly and interact with stem-loop IIa of U2 snRNA to promote U2 snRNP association with pre-mRNA. In vitro spliceosome assembly assay; genetic epistasis; biochemical complementation Genes & development High 8405998
1994 The SURP (surp) module is a conserved motif shared between PRP21/SF3A1-family constitutive splicing proteins and SWAP alternative splicing regulators across metazoans, defining two ancient protein families that act at the same early step in prespliceosome assembly. Sequence analysis; genetic/evolutionary comparison; functional classification based on splicing phenotypes Nucleic acids research Medium 7971282
1995 SF3A120 (SF3A1) is identified as the mammalian homolog of yeast PRP21p. Its N-terminal half contains tandemly repeated SURP modules that mediate binding to SF3A60, while a region C-terminal to the SURP modules contacts SF3A66. The C-terminal half contains a proline-rich region and a ubiquitin-like domain. SF3a complex (SF3A1 + SF3A60 + SF3A66) converts U2 snRNP into its active form. cDNA cloning; binding studies with truncated SF3A120 derivatives; chromosomal localization RNA (New York, N.Y.) High 7489498
1996 Prp9, Prp11, and Prp21 (SF3A1 ortholog) form a direct trimeric protein complex (Prp9·Prp11·Prp21) that is functional in in vitro splicing. This complex alters the structure of U2 snRNP, rendering the branch-point pairing region of U2 snRNA more accessible to oligonucleotide-directed RNase H cleavage, suggesting a role in activating U2 snRNP for prespliceosome assembly. Protein expression in E. coli; metal affinity chromatography purification; in vitro splicing assay; oligonucleotide-directed RNase H accessibility assay The Journal of biological chemistry High 8969185
1996 Heat-sensitive prp21 point mutations reveal that specific domains of Prp21p are required for interaction with Prp9p (but not Prp11p), and these domains are conserved across evolution. Defects in Prp9p interaction correlate with both splicing defects and pre-mRNA nuclear export phenotype. The surp1 module is dispensable for yeast viability under standard conditions, suggesting an as-yet-unknown function for this most conserved motif. Genetic mutagenesis; temperature-sensitive mutant analysis; deletion analysis; in vivo pre-mRNA accumulation assays RNA (New York, N.Y.) High 8718683
1996 Genetic interaction between PRP21 (SF3A1 ortholog, component of U2 snRNP) and PRP24 (component of U6 snRNP) was established by allele-specific extragenic suppression: a prp21-2 mutation fully suppresses splicing defects of prp24-1 and restores U6 snRNA levels, indicating functional communication between U2 and U6 snRNP components. Genetic suppressor screen; in vivo pre-mRNA splicing analysis; genetic complementation Molecular & general genetics : MGG Medium 8602141
2001 All three SF3a subunits (SF3A60, SF3A66, SF3A120/SF3A1) are essential for formation of the mature 17S U2 snRNP and prespliceosome. Within the SF3a heterotrimer, SF3A60 and SF3A66 each interact with SF3A120 but not with each other. SF3A60 plays a major role in recruiting SF3A120 into the U2 particle. N-terminal portions of SF3A60 and SF3A66 contain SF3A120 interaction sites. C2H2-type zinc finger domains in SF3A60 and SF3A66 mediate integration into U2 snRNP, likely through contacts with Sm proteins. Recombinant protein expression in insect cells; in vitro U2 snRNP assembly assay; prespliceosome formation assay; domain deletion analysis Molecular and cellular biology High 11533230
2014 SF3A1 (a U2 snRNP protein) directly interacts with stem-loop 4 (SL4) of U1 snRNA during prespliceosomal complex assembly on pre-mRNA. This interaction bridges the 5' and 3' splice site complexes within the assembling spliceosome. Free U1-SL4 RNA added to splicing reactions inhibits splicing and blocks assembly prior to A complex formation, demonstrating a functional requirement for this contact. SILAC-based quantitative mass spectrometry; biotin/Neutravidin affinity pull-down; U1 snRNP complementation assay; in vitro splicing inhibition assay; complex assembly analysis Genes & development High 25403181
2019 The ubiquitin-like (UBL) domain at the C-terminus of SF3A1 functions as a noncanonical RNA binding domain that directly binds the stem-loop 4 (SL4) of U1 snRNA with high affinity (KD ~97 nM). The double-stranded G-C rich stem of U1-SL4 is an important feature for binding. Two conserved tyrosine residues, Y772 and Y773, contribute critically to binding affinity. SF3A1-UBL can pull down the intact U1 snRNP from HeLa nuclear extract. UV-crosslinking with 32P-labeled RNA using deletion constructs; electrophoretic mobility shift assay (EMSA); surface plasmon resonance; site-directed mutagenesis; pull-down from HeLa nuclear extract RNA (New York, N.Y.) High 31383795
2022 The NMR solution structure of the SF3A1 SURP1 domain in complex with a human SF1 fragment was determined. SURP1 adopts a canonical α1-α2-310-α3 topology where α1 and α2 are fixed at an acute angle by a single glycine residue. A hydrophobic patch on α1/α2 contacts a hydrophobic cluster on a 16-residue α-helix of SF1. The interaction is transient (KD ~20 μM), involving both hydrophobic contacts and salt bridges/hydrogen bonds, consistent with a transient recruitment of U2 snRNP to early spliceosomal complexes. SURP2, by contrast, is permanently associated with SF3A3. NMR structure determination; bio-layer interferometry; mutational analysis Protein science : a publication of the Protein Society High 36173164
2023 The 1.80 Å crystal structure of the SF3A1 ubiquitin-like domain (ULD, residues 704–793) complexed with U1 snRNA SL4 (UUCG tetraloop) reveals a β-grasp fold (β1-β2-α1-310a-β3-β4-310b-β5). Three ULD-specific residues (Lys756, Phe763, Lys765) contact the canonical UUCG tetraloop structure, while the C-terminal tail (786KERGGRKK793) adopts a stretched conformation with its main/side chains contacting the major groove of the stem helix via RGG residues. Putative post-translational modifications including ubiquitination within the ULD would directly inhibit SL4 binding. X-ray crystallography (1.80 Å); bio-layer interferometry; mutational analysis Journal of biochemistry High 37094335
2024 SF3A1, an essential spliceosomal component, interacts with NCBP1. Electrophile modification of NCBP1 at a single cysteine (C436) impairs its association with SF3A1, triggering alternative splicing of >250 genes including S6K1, whose alternatively-spliced form dominantly inhibits protein translation. Precision localized electrophile generation; genetic code expansion; protein-protein interaction assay; RNA sequencing for alternative splicing; functional translation assays bioRxivpreprint Medium bio_10.1101_2024.05.12.593755
2025 SF3A1 was identified as a direct molecular target of hydroxysafflor yellow A (HSYA) by thermal proteome profiling. Silencing SF3A1 impairs mitochondrial energy metabolism and abolishes HSYA-mediated protective effects against myocardial ischemia/reperfusion injury, including ROS clearance, restoration of mitochondrial polarization/membrane potential, and promotion of oxidative phosphorylation and ATP synthesis. Thermal proteome profiling (target identification); RNA sequencing; siRNA knockdown; mitochondrial function assays (ROS, membrane potential, ATP synthesis); in vivo mouse myocardial infarction model European journal of pharmacology Medium 40449648

Source papers

Stage 0 corpus · 48 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2861 17081983
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2006 A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 1362 16751776
2010 Network organization of the human autophagy system. Nature 1286 20562859
2009 Defining the human deubiquitinating enzyme interaction landscape. Cell 1282 19615732
2004 Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Sciences of the United States of America 1159 15302935
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2012 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular cell 973 22681889
2004 Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nature biotechnology 916 15592455
2018 VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell discovery 829 29507755
1999 The DNA sequence of human chromosome 22. Nature 808 10591208
2008 Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 787 18854154
2007 Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular systems biology 733 17353931
2002 Comprehensive proteomic analysis of the human spliceosome. Nature 725 12226669
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2005 High-throughput mapping of a dynamic signaling network in mammalian cells. Science (New York, N.Y.) 553 15761153
2017 Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science (New York, N.Y.) 533 28302793
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2010 Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (New York, N.Y.) 421 20360068
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
1998 Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nature genetics 404 9731529
1996 Normalization and subtraction: two approaches to facilitate gene discovery. Genome research 401 8889548
2007 Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Molecular cell 367 17643375
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
1993 Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA. Genes & development 125 8405998
2014 Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly. Genes & development 56 25403181
1995 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. RNA (New York, N.Y.) 55 7489498
2001 Domains in human splicing factors SF3a60 and SF3a66 required for binding to SF3a120, assembly of the 17S U2 snRNP, and prespliceosome formation. Molecular and cellular biology 48 11533230
1993 The Saccharomyces cerevisiae PRP21 gene product is an integral component of the prespliceosome. Proceedings of the National Academy of Sciences of the United States of America 43 8341697
1996 In vitro studies of the Prp9.Prp11.Prp21 complex indicate a pathway for U2 small nuclear ribonucleoprotein activation. The Journal of biological chemistry 35 8969185
1994 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. Nucleic acids research 27 7971282
2019 Identification of a noncanonical RNA binding domain in the U2 snRNP protein SF3A1. RNA (New York, N.Y.) 21 31383795
2015 SF3A1 and pancreatic cancer: new evidence for the association of the spliceosome and cancer. Oncotarget 19 26498691
1994 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. Yeast (Chichester, England) 16 7754713
1996 Essential domains of the PRP21 splicing factor are implicated in the binding to PRP9 and PRP11 proteins and are conserved through evolution. RNA (New York, N.Y.) 13 8718683
2022 Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1. Protein science : a publication of the Protein Society 12 36173164
2015 The Associations between RNA Splicing Complex Gene SF3A1 Polymorphisms and Colorectal Cancer Risk in a Chinese Population. PloS one 8 26079486
1999 A mutation in a methionine tRNA gene suppresses the prp2-1 Ts mutation and causes a pre-mRNA splicing defect in Saccharomyces cerevisiae. Genetics 6 10545445
1996 An extragenic suppressor of prp24-1 defines genetic interaction between PRP24 and PRP21 gene products of Saccharomyces cerevisiae. Molecular & general genetics : MGG 4 8602141
2023 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. Journal of biochemistry 2 37094335
2025 SF3a1: A Novel Potential Tumor Biomarker or Therapeutic Target. Journal of Cancer 1 40302801
2025 Hydroxysafflor yellow A alleviates ischemic myocardial injury by targeting SF3A1 to improve mitochondrial energy metabolism. European journal of pharmacology 0 40449648