1FYR

DIMER FORMATION THROUGH DOMAIN SWAPPING IN THE CRYSTAL STRUCTURE OF THE GRB2-SH2 AC-PYVNV COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex.

Schiering, N.Casale, E.Caccia, P.Giordano, P.Battistini, C.

(2000) Biochemistry 39: 13376-13382


  • PubMed Abstract: 
  • Src homology 2 (SH2) domains are key modules in intracellular signal transduction. They link activated cell surface receptors to downstream targets by binding to phosphotyrosine-containing sequence motifs. The crystal structure of a Grb2-SH2 domain-p ...

    Src homology 2 (SH2) domains are key modules in intracellular signal transduction. They link activated cell surface receptors to downstream targets by binding to phosphotyrosine-containing sequence motifs. The crystal structure of a Grb2-SH2 domain-phosphopeptide complex was determined at 2.4 A resolution. The asymmetric unit contains four polypeptide chains. There is an unexpected domain swap so that individual chains do not adopt a closed SH2 fold. Instead, reorganization of the EF loop leads to an open, nonglobular fold, which associates with an equivalent partner to generate an intertwined dimer. As in previously reported crystal structures of canonical Grb2-SH2 domain-peptide complexes, each of the four hybrid SH2 domains in the two domain-swapped dimers binds the phosphopeptide in a type I beta-turn conformation. This report is the first to describe domain swapping for an SH2 domain. While in vivo evidence of dimerization of Grb2 exists, our SH2 dimer is metastable and a physiological role of this new form of dimer formation remains to be demonstrated.


    Organizational Affiliation

    Department of Structural Chemistry, Discovery Research Oncology, Viale Pasteur 10, 20014 Nerviano (MI), Italy. nikolaus.schiering@eu.pnu.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
A, B, C, D
114Homo 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
HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
I, J, K, L
5Homo sapiensMutation(s): 0 
Gene Names: MET
EC: 2.7.10.1
Find proteins for P08581 (Homo sapiens)
Go to Gene View: MET
Go to UniProtKB:  P08581
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
I, J, K, L
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
ACE
Query on ACE
I, J, K, L
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.610α = 90.00
b = 77.610β = 90.00
c = 183.470γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance