SF3A1

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).

1. 1993 High

   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

   PMID:8341697 PMID:8405998

   Open questions at the time

   • Did not resolve which contacts are direct RNA vs protein
   • Mammalian counterpart not yet tested
   • Order of subunit recruitment unresolved
2. 1996 High

   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

   PMID:8718683 PMID:8969185

   Open questions at the time

   • Mechanism of how U2 branch-point region is remodeled unresolved
   • SURP1 role not addressed by these interactions
   • Export phenotype mechanism unexplained
3. 1996 Medium

   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

   PMID:8602141

   Open questions at the time

   • Genetic interaction only, no direct biochemical validation
   • Physical basis of U2-U6 link not established
   • Relevance to human SF3A1 untested
4. 2001 High

   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

   PMID:11533230

   Open questions at the time

   • Did not address SF3A1 contacts to other snRNPs
   • Stoichiometry within U2 not fully resolved
   • Dynamics of assembly not captured
5. 2014 High

   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

   PMID:25403181

   Open questions at the time

   • Which SF3A1 domain mediates SL4 binding not yet mapped
   • Structural basis of recognition unknown
   • In vivo requirement not directly tested
6. 2019 High

   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

   PMID:31383795

   Open questions at the time

   • Atomic-resolution interface not yet defined
   • Regulation of the interaction unknown
   • Effect of UBL mutations in cells untested
7. 2022 High

   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)

   PMID:36173164

   Open questions at the time

   • 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
8. 2023 High

   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

   PMID:37094335

   Open questions at the time

   • Predicted regulatory ubiquitination not experimentally confirmed
   • Structure of full SF3A1 within U2 snRNP context lacking
   • Dynamics of bridge formation/release not captured

• 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.
• 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