4FXW

Structure of phosphorylated SF1 complex with U2AF65-UHM domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex.

Wang, W.Maucuer, A.Gupta, A.Manceau, V.Thickman, K.R.Bauer, W.J.Kennedy, S.D.Wedekind, J.E.Green, M.R.Kielkopf, C.L.

(2013) Structure 21: 197-208

  • DOI: 10.1016/j.str.2012.10.020
  • Primary Citation of Related Structures:  
    4FXW, 4FXX

  • PubMed Abstract: 
  • The essential splicing factors U2AF⁶⁵ and SF1 cooperatively bind consensus sequences at the 3' end of introns. Phosphorylation of SF1 on a highly conserved "SPSP" motif enhances its interaction with U2AF⁶⁵ and the pre-mRNA. Here, we reveal that phosphorylation induces essential conformational changes in SF1 and in the SF1/U2AF⁶⁵/3' splice site complex ...

    The essential splicing factors U2AF⁶⁵ and SF1 cooperatively bind consensus sequences at the 3' end of introns. Phosphorylation of SF1 on a highly conserved "SPSP" motif enhances its interaction with U2AF⁶⁵ and the pre-mRNA. Here, we reveal that phosphorylation induces essential conformational changes in SF1 and in the SF1/U2AF⁶⁵/3' splice site complex. Crystal structures of the phosphorylated (P)SF1 domain bound to the C-terminal domain of U2AF⁶⁵ at 2.29 Å resolution and of the unphosphorylated SF1 domain at 2.48 Å resolution demonstrate that phosphorylation induces a disorder-to-order transition within a previously unknown SF1/U2AF⁶⁵ interface. We find by small-angle X-ray scattering that the local folding of the SPSP motif transduces into global conformational changes in the nearly full-length (P)SF1/U2AF⁶⁵/3' splice site assembly. We further determine that SPSP phosphorylation and the SF1/U2AF⁶⁵ interface are essential in vivo. These results offer a structural prototype for phosphorylation-dependent control of pre-mRNA splicing factors.


    Organizational Affiliation

    Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 65 kDa subunitA, C106Homo sapiensMutation(s): 0 
Gene Names: U2AF2U2AF65
UniProt & NIH Common Fund Data Resources
Find proteins for P26368 (Homo sapiens)
Explore P26368 
Go to UniProtKB:  P26368
PHAROS:  P26368
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 1B, D124Homo sapiensMutation(s): 0 
Gene Names: SF1ZFM1ZNF162
UniProt & NIH Common Fund Data Resources
Find proteins for Q15637 (Homo sapiens)
Explore Q15637 
Go to UniProtKB:  Q15637
PHAROS:  Q15637
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
SEP
Query on SEP
B, DL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.8α = 90
b = 116.1β = 90
c = 130γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description