1GCQ

CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel recognition mode between Vav and Grb2 SH3 domains.

Nishida, M.Nagata, K.Hachimori, Y.Horiuchi, M.Ogura, K.Mandiyan, V.Schlessinger, J.Inagaki, F.

(2001) EMBO J. 20: 2995-3007

  • DOI: 10.1093/emboj/20.12.2995
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vav is a guanine nucleotide exchange factor for the Rho/Rac family that is expressed exclusively in hematopoietic cells. Growth factor receptor-bound protein 2 (Grb2) has been proposed to play important roles in the membrane localization and activati ...

    Vav is a guanine nucleotide exchange factor for the Rho/Rac family that is expressed exclusively in hematopoietic cells. Growth factor receptor-bound protein 2 (Grb2) has been proposed to play important roles in the membrane localization and activation of Vav through dimerization of its C-terminal Src-homology 3 (SH3) domain (GrbS) and the N-terminal SH3 domain of Vav (VavS). The crystal structure of VavS complexed with GrbS has been solved. VavS is distinct from other SH3 domain proteins in that its binding site for proline-rich peptides is blocked by its own RT loop. One of the ends of the VavS beta-barrel forms a concave hydrophobic surface. The GrbS components make a contiguous complementary interface with the VavS surface. The binding site of GrbS for VavS partially overlaps with the canonical binding site for proline-rich peptides, but is definitely different. Mutations at the interface caused a decrease in the binding affinity of VavS for GrbS by 4- to 40-fold. The structure reveals how GrbS discriminates VavS specifically from other signaling molecules without binding to the proline-rich motif.


    Organizational Affiliation

    Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-12, W-6, Kita-ku, Sapporo 060-0812, CREST, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
A, B
61Homo sapiensMutation(s): 0 
Gene Names: GRB2 (ASH)
Find proteins for P62993 (Homo sapiens)
Go to Gene View: GRB2
Go to UniProtKB:  P62993
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VAV PROTO-ONCOGENE
C
70Mus musculusMutation(s): 0 
Gene Names: Vav1 (Vav)
Find proteins for P27870 (Mus musculus)
Go to UniProtKB:  P27870
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 48.050α = 90.00
b = 126.820β = 90.00
c = 83.370γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
MLPHAREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance