Affinage

SF3B5

Splicing factor 3B subunit 5 · UniProt Q9BWJ5

Round 2 corrected
Length
86 aa
Mass
10.1 kDa
Annotated
2026-04-28
40 papers in source corpus 11 papers cited in narrative 11 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SF3B5 (SF3b10) is a constitutive structural subunit of the heptameric SF3b complex within the U2 snRNP, functioning as a core scaffold throughout the spliceosome assembly and activation cycle. Identified as a stoichiometric component of purified spliceosomes and the 17S U2 snRNP (PMID:12226669, PMID:12234937), SF3B5 directly contacts SF3B1 and helps maintain the HEAT-domain superhelix in an open conformation in the free U2 snRNP, which transitions to a closed state upon branch-point adenosine engagement during spliceosome assembly (PMID:27720643, PMID:32494006). Structural studies across successive spliceosomal intermediates—prespliceosomal A, pre-B, B, and Bact complexes—confirm that SF3B5 remains stably integrated throughout these stages (PMID:17332742, PMID:30975767, PMID:28781166, PMID:29360106). The SF3B5-containing SF3b pocket is the binding site for competitive splicing modulators such as E7107, which occupy the branch-point adenosine-binding pocket to inhibit splicing (PMID:29491137).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2002 High

    The discovery that SF3B5 is a bona fide subunit of both the SF3b subcomplex and intact spliceosomes established it as a previously unrecognized spliceosomal component, opening the question of its structural and functional role within the U2 snRNP.

    Evidence Mass spectrometry of affinity-purified human spliceosomes and immunoprecipitated SF3b/17S U2 snRNP

    PMID:12226669 PMID:12234937

    Open questions at the time
    • No direct contacts with other SF3b subunits were mapped
    • No functional assay (e.g. depletion/reconstitution) was performed for SF3B5 specifically
    • Subcellular localization was inferred from the SF3b complex, not SF3B5 directly
  2. 2007 High

    Detection of SF3B5 in stoichiometric amounts within prespliceosomal A complexes demonstrated that the subunit is incorporated at the earliest stage of spliceosome assembly, before catalytic activation.

    Evidence Double-affinity purification of human A complexes under physiological conditions with MS and EM

    PMID:17332742

    Open questions at the time
    • Whether SF3B5 makes direct contacts with pre-mRNA or other A-complex factors was unknown
    • No structure was available to explain how SF3B5 is positioned within the A complex
  3. 2016 High

    The crystal structure of the SF3b core complex resolved how SF3B5 directly contacts SF3B1's HEAT-domain superhelix and contributes to the scaffold that positions the branch-site recognition platform, answering the long-standing question of its structural role.

    Evidence X-ray crystallography of the human SF3b core complex with crosslinking MS validation; complementary cryo-EM-guided integrative modeling

    PMID:27618338 PMID:27720643

    Open questions at the time
    • The open-versus-closed conformational dynamics of SF3B1 HEAT domain in the context of U2 snRNP were not yet resolved
    • Functional consequences of disrupting the SF3B5–SF3B1 interface were not tested by mutagenesis
  4. 2017 High

    Cryo-EM visualization of the pre-catalytic B complex placed SF3B5 within the U2 snRNP head domain connected to the spliceosome body, establishing its persistence beyond prespliceosomal stages.

    Evidence Cryo-EM structure of human pre-catalytic B complex spliceosome

    PMID:28781166

    Open questions at the time
    • Whether SF3B5 makes stage-specific contacts that change between A and B complexes was unresolved
    • Resolution was insufficient to define SF3B5 side-chain interactions
  5. 2018 High

    Structures of the SF3b–E7107 complex and the activated Bact spliceosome together revealed that SF3B5 forms part of the drug-target pocket and remains stably associated through the B-to-Bact transition, linking the subunit to both pharmacological inhibition of splicing and the full activation pathway.

    Evidence Cryo-EM of SF3b–E7107 at 3.95 Å with SAR analysis; cryo-EM of human Bact in three conformational states with atomic modeling

    PMID:29360106 PMID:29491137

    Open questions at the time
    • Whether SF3B5 depletion alone affects drug sensitivity was not tested
    • The exact contribution of SF3B5 to the open-to-closed conformational switch was not isolated from SF3B1 contributions
  6. 2019 High

    Near-atomic resolution structure of the human pre-B spliceosome confirmed SF3B5 is present at the earliest tri-snRNP engagement stage, completing the picture of SF3B5 occupancy across all major assembly intermediates (A → pre-B → B → Bact).

    Evidence Cryo-EM of human pre-B spliceosome at 3.3 Å core resolution

    PMID:30975767

    Open questions at the time
    • Dynamics of SF3B5 release during the Bact-to-C transition were not captured
    • No kinetic or thermodynamic measurements of SF3B5 binding to SF3B1 in the context of assembly intermediates
  7. 2020 High

    The 17S U2 snRNP structure showed that SF3B1's HEAT domain—scaffolded by SF3B5—adopts an open conformation in the free snRNP, resolving why conformational remodeling is required for branch-site recognition and providing the structural basis for SF3B5's role in enabling this transition.

    Evidence Cryo-EM of human 17S U2 snRNP at 4.1 Å with protein crosslinking MS

    PMID:32494006

    Open questions at the time
    • No mutagenesis or depletion/reconstitution experiment has isolated SF3B5's specific contribution to the open-to-closed transition
    • Whether SF3B5 has functions outside the canonical spliceosome cycle remains untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • The direct functional consequence of SF3B5 loss on splicing activity in human cells has not been demonstrated by targeted depletion or mutagenesis, leaving the question of whether it is an essential or modulatory subunit unresolved at the biochemical level.
  • No depletion/knockdown or reconstitution experiment for SF3B5 in a human system
  • No disease-causing mutations in SF3B5 have been reported
  • The precise energetic contribution of SF3B5 to SF3b complex stability is unmeasured

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 5
Localization
GO:0005634 nucleus 2 GO:0005654 nucleoplasm 2
Pathway
R-HSA-8953854 Metabolism of RNA 7
Partners
PHF5ASF3B1SF3B14SF3B2SF3B3SF3B4SF3B6
Complex memberships
SF3b complexU2 snRNP

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2002 SF3B5 (SF3b10) was identified as a bona fide protein component of the human SF3b subcomplex of the U2 snRNP and of intact functional spliceosomes, as determined by mass spectrometry of purified spliceosomal particles. Maltose-binding protein affinity chromatography combined with nanoscale LC-MS/MS mass spectrometry of purified functional human spliceosomes Nature High 12226669
2002 SF3B5 (SF3b10) was identified as a stable component of both SF3b and the 17S U2 snRNP by mass spectrometry; immunofluorescence/FISH studies placed SF3b155 (but not SF3b10/SF3B5 specifically) outside Cajal bodies, providing initial subcellular context for SF3b assembly. Mass spectrometry of immunoprecipitated SF3b and 17S U2 snRNP; immunofluorescence and FISH The EMBO journal High 12234937
2007 SF3B5 (SF3b10) was detected as a stoichiometric component of human prespliceosomal A complexes, demonstrating its stable incorporation at an early stage of spliceosome assembly before catalytic activation. Double-affinity purification of prespliceosomal A complexes under physiological conditions followed by mass spectrometry and EM The EMBO journal High 17332742
2009 In Trypanosoma brucei, the SF3B5 ortholog (as part of the SF3b complex) co-purifies with homologues of p14, SAP130, SAP145, and SAP155, and localizes to the nucleus; RNAi knockdown of the associated SAP49 homologue (DRBD1) inhibited trypanosome growth and caused splicing defects, demonstrating conserved functional importance of the SF3b complex including SF3B5. TAP-tag co-purification mass spectrometry, immunofluorescence localization, RNAi knockdown with growth and splicing phenotype readout in T. brucei Molecular and biochemical parasitology Medium 19450735
2016 Crystal structure of the human SF3b core complex revealed that SF3B5 (SF3b10) directly contacts SF3B1 (SF3b155) and contributes to maintaining the distinctive conformation of the SF3B1 HEAT domain superhelix; SF3B5 forms part of the structural scaffold that positions the branch-site recognition platform. X-ray crystallography of the human SF3b core complex (crystal structure); protein-protein crosslinking mass spectrometry Molecular cell High 27720643
2016 Integrative cryo-EM-guided modeling localized SF3B5 (SF3b10) within the closed form of the SF3b complex for the first time, placing it in spatial proximity to SF3b155, SF3b145, SF3b130, and SF3b14b and identifying a hinge region in SF3b155 important for the open-to-closed conformational transition relevant to branch-point adenosine recognition. Integrative structural modeling guided by cryo-EM density maps, comparative homology modeling, and experimental data RNA biology Medium 27618338
2017 In the cryo-EM structure of the pre-catalytic human spliceosomal B complex, SF3B5 is present as a stable SF3b component within the U2 snRNP head domain, which connects to the B complex main body via three bridges, positioning SF3b for subsequent activation steps. Cryo-EM structure of the pre-catalytic human B complex spliceosome Cell High 28781166
2018 Cryo-EM structure of the SF3b subcomplex (comprising SF3B1, SF3B3, PHF5A, and SF3B5) bound to the splicing modulator E7107 at 3.95 Å revealed that SF3B5 is an integral structural subunit of the drug-bound complex; the structure showed E7107 occupies the branch-point adenosine-binding pocket, supporting a substrate-competitive mechanism of action for splicing modulators. Cryo-EM structure determination of SF3b–E7107 complex; structure-activity relationship analysis with chemical probes; functional assays with strong vs. weak pre-mRNA substrates Genes & development High 29491137
2018 In the cryo-EM structures of the human activated spliceosome (Bact complex), atomic models of all seven SF3b subunits including SF3B5 were built, confirming SF3B5 as a structural component maintained throughout spliceosome activation; the three conformational states captured revealed that SF3b remains stably associated through the B-to-Bact transition. Cryo-EM structure of human Bact complex in three conformational states with atomic modeling of SF3b subunits Cell research High 29360106
2019 Cryo-EM structure of the human pre-B spliceosome complex showed SF3B5 as part of the SF3b module within U2 snRNP, and the structures collectively demonstrate that the SF3b complex including SF3B5 is positioned to interact with the branch-point sequence as part of the pre-mRNA recognition machinery before catalytic activation. Cryo-EM structure of human pre-B spliceosome at 3.3 Å core resolution Science High 30975767
2020 Cryo-EM structure of the human 17S U2 snRNP at 4.1 Å core resolution, combined with protein crosslinking data, revealed the molecular architecture of the snRNP and showed that SF3B1's HEAT domain (which is scaffolded in part by SF3B5) maintains an open conformation in isolated U2 snRNP, in contrast to the closed conformation observed in assembled spliceosomes, explaining why BSL remodeling is required for stable U2–branch-site interaction. Cryo-EM structure determination of 17S U2 snRNP; protein crosslinking mass spectrometry Nature High 32494006

Source papers

Stage 0 corpus · 40 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
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
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
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2000 DNA cloning using in vitro site-specific recombination. Genome research 815 11076863
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
2010 Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 639 20850016
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
2001 Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Molecular and cellular biology 320 11564863
2008 A TFTC/STAGA module mediates histone H2A and H2B deubiquitination, coactivates nuclear receptors, and counteracts heterochromatin silencing. Molecular cell 307 18206972
2000 Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO reports 281 11256614
2016 The cell proliferation antigen Ki-67 organises heterochromatin. eLife 265 26949251
2017 A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Molecular cell 248 28431233
2003 The DNA sequence and analysis of human chromosome 6. Nature 242 14574404
2002 Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. The EMBO journal 237 12234937
2016 Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations. Molecular cell 209 27720643
2017 Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. Cell 199 28781166
2020 Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. Nature cell biology 194 32203420
2018 Structure of the human activated spliceosome in three conformational states. Cell research 176 29360106
2013 The protein interaction landscape of the human CMGC kinase group. Cell reports 174 23602568
2020 UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nature cell biology 168 32807901
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2007 Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes. The EMBO journal 161 17332742
2019 Mechanism of 5' splice site transfer for human spliceosome activation. Science (New York, N.Y.) 141 30975767
2018 The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action. Genes & development 98 29491137
2020 Molecular architecture of the human 17S U2 snRNP. Nature 83 32494006
2016 Approaches to Investigating Complex Genetic Traits in a Large-Scale Inbred Mouse Aging Study. Veterinary pathology 22 26936752
2021 WGCNA-Based Identification of Hub Genes and Key Pathways Involved in Nonalcoholic Fatty Liver Disease. BioMed research international 20 34938809
2022 Comprehensive transcriptomics and proteomics analysis of Carassius auratus gills in response to Aeromonas hydrophila. Fish and shellfish immunology reports 12 36589261
2009 DRBD1 is the Trypanosoma brucei homologue of the spliceosome-associated protein 49. Molecular and biochemical parasitology 8 19450735
2016 Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. RNA biology 7 27618338
2020 Transcriptome complexity in intravascular NK/T-cell lymphoma. Journal of clinical pathology 4 32188628
2025 Expansion of the functional genomics GRACE library reveals genes relevant for temperature-dependent fitness in Candida albicans. PLoS biology 1 41105619