2H5K

Crystal Structure of Complex Between the Domain-Swapped Dimeric Grb2 SH2 Domain and Shc-Derived Ligand, Ac-NH-pTyr-Val-Asn-NH2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and energetic aspects of Grb2-SH2 domain-swapping.

Benfield, A.P.Whiddon, B.B.Clements, J.H.Martin, S.F.

(2007) Arch.Biochem.Biophys. 462: 47-53

  • DOI: 10.1016/j.abb.2007.03.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The SH2 domain of growth factor receptor-bound protein 2 (Grb2) has been the focus of numerous studies, primarily because of the important roles it plays in signal transduction. More recently, it has emerged as a useful protein to study the consequen ...

    The SH2 domain of growth factor receptor-bound protein 2 (Grb2) has been the focus of numerous studies, primarily because of the important roles it plays in signal transduction. More recently, it has emerged as a useful protein to study the consequences of ligand preorganization upon energetics and structure in protein-ligand interactions. The Grb2-SH2 domain is known to form a domain-swapped dimer, and as part of our investigations toward correlating structure and energetics in biological systems, we examined the effects that domain-swapping dimerization of the Grb2-SH2 domain had upon ligand binding affinities. Isothermal titration calorimetry was performed using Grb2-SH2 in both its monomeric and domain-swapped dimeric forms and a phosphorylated tripeptide AcNH-pTyr-Val-Asn-NH(2) that is similar to the Shc sequence recognized by Grb2-SH2 in vivo. The two binding sites of domain-swapped dimer exhibited a 4- and a 13-fold reduction in ligand affinity compared to monomer. Crystal structures of peptide-bound and uncomplexed forms of Grb2-SH2 domain-swapped dimer were obtained and reveal that the orientation of residues V122, V123, and R142 may influence the conformation of W121, an amino acid that is believed to play an important role in Grb2-SH2 ligand sequence specificity. These findings suggest that domain-swapping of Grb2-SH2 not only results in a lower affinity for a Shc-derived ligand, but it may also affect ligand specificity.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth factor receptor-bound protein 2
A, B
116Homo 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
Shc-Derived Ligand
C
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download SDF File 
Download CCD File 
B
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C
NON-POLYMERH2 N

--

PTR
Query on PTR
C
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
ACE
Query on ACE
C
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.247 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.859α = 90.00
b = 94.859β = 90.00
c = 139.236γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
MOLREPphasing
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description