4DGW

Crystal Structure of the SF3a splicing factor complex of U2 snRNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.233 

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Literature

Structure and assembly of the SF3a splicing factor complex of U2 snRNP

Lin, P.C., Xu, R.M.

(2012) EMBO J 31: 1579-1590

  • DOI: 10.1038/emboj.2012.7
  • Primary Citation of Related Structures:  
    4DGW

  • PubMed Abstract: 

    • SF3a is an evolutionarily conserved heterotrimeric complex essential for pre-mRNA splicing. It functions in spliceosome assembly within the mature U2 snRNP (small nuclear ribonucleoprotein particle), and its displacement from the spliceosome initiates the first step of the splicing reaction ...

    SF3a is an evolutionarily conserved heterotrimeric complex essential for pre-mRNA splicing. It functions in spliceosome assembly within the mature U2 snRNP (small nuclear ribonucleoprotein particle), and its displacement from the spliceosome initiates the first step of the splicing reaction. We have identified a core domain of the yeast SF3a complex required for complex assembly and determined its crystal structure. The structure shows a bifurcated assembly of three subunits, Prp9, Prp11 and Prp21, with Prp9 interacting with Prp21 via a bidentate-binding mode, and Prp21 wrapping around Prp11. Structure-guided biochemical analysis also shows that Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA. These findings provide mechanistic insights into the assembly of U2 snRNP.

    Organizational Affiliation: 

    Structural Biology Program, The Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and the Department of Pharmacology, New York University School of Medicine, New York, NY, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP9A402Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP9, YDL030W, D2773
UniProt
Find proteins for P19736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P19736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19736
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP21B152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP21, SPP91, YJL203W, J0322
UniProt
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32524
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UniProt GroupP32524
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP11C231Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: PRP11, PRP10, RNA11, YDL043C, D2711
UniProt
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07350 
Go to UniProtKB:  Q07350
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07350
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.233 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.781α = 90
b = 127.259β = 90
c = 169.173γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-01-26 
  • Released Date: 2012-05-02 
    • Deposition Author(s): Lin, P.C.

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Source and taxonomy, Structure summary