3BEG

Crystal structure of SR protein kinase 1 complexed to its substrate ASF/SF2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by SRPK1

Ngo, J.C.Giang, K.Chakrabarti, S.Ma, C.-T.Huynh, N.Hagopian, J.Dorrestein, P.C.Fu, X.-D.Adams, J.A.Ghosh, G.

(2008) Mol Cell 29: 563-576

  • DOI: 10.1016/j.molcel.2007.12.017
  • Primary Citation of Related Structures:  
    3BEG

  • PubMed Abstract: 
  • The 2.9 A crystal structure of the core SRPK1:ASF/SF2 complex reveals that the N-terminal half of the basic RS domain of ASF/SF2, which is destined to be phosphorylated, is bound to an acidic docking groove of SRPK1 distal to the active site. Phosphorylation of ASF/SF2 at a single site in the C-terminal end of the RS domain generates a primed phosphoserine that binds to a basic site in the kinase ...

    The 2.9 A crystal structure of the core SRPK1:ASF/SF2 complex reveals that the N-terminal half of the basic RS domain of ASF/SF2, which is destined to be phosphorylated, is bound to an acidic docking groove of SRPK1 distal to the active site. Phosphorylation of ASF/SF2 at a single site in the C-terminal end of the RS domain generates a primed phosphoserine that binds to a basic site in the kinase. Biochemical experiments support a directional sliding of the RS peptide through the docking groove to the active site during phosphorylation, which ends with the unfolding of a beta strand of the RRM domain and binding of the unfolded region to the docking groove. We further suggest that the priming of the first serine facilitates directional substrate translocation and efficient phosphorylation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase SRPK1 A381Homo sapiensMutation(s): 0 
Gene Names: SRPK1
EC: 2.7.11.1
Find proteins for Q96SB4 (Homo sapiens)
Explore Q96SB4 
Go to UniProtKB:  Q96SB4
NIH Common Fund Data Resources
PHAROS:  Q96SB4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor, arginine/serine-rich 1 B115Homo sapiensMutation(s): 0 
Gene Names: SFRS1ASFSF2SF2P33SRSF1OK/SW-cl.3
Find proteins for Q07955 (Homo sapiens)
Explore Q07955 
Go to UniProtKB:  Q07955
NIH Common Fund Data Resources
PHAROS:  Q07955
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
SEP
Query on SEP

Download Ideal Coordinates CCD File 
A
PHOSPHOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
 Ligand Interaction
ALA
Query on ALA

Download Ideal Coordinates CCD File 
A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.406α = 90
b = 117.525β = 90
c = 193.554γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-09-10
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2017-10-25
    Changes: Refinement description