3WA4

Grb2 SH2 domain/CD28-derived peptide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report



Literature

High Resolution Crystal Structure of the Grb2 SH2 Domain with a Phosphopeptide Derived from CD28

Higo, K., Ikura, T., Oda, M., Morii, H., Takahashi, J., Abe, R., Ito, N.

(2013) PLoS One 8: e74482-e74482

  • DOI: 10.1371/journal.pone.0074482
  • Primary Citation of Related Structures:  
    3WA4

  • PubMed Abstract: 

    • Src homology 2 (SH2) domains play a critical role in cellular signal transduction. They bind to peptides containing phosphotyrosine (pY) with various specificities that depend on the flanking amino-acid residues. The SH2 domain of growth-factor recep ...

    Src homology 2 (SH2) domains play a critical role in cellular signal transduction. They bind to peptides containing phosphotyrosine (pY) with various specificities that depend on the flanking amino-acid residues. The SH2 domain of growth-factor receptor-bound protein 2 (Grb2) specifically recognizes pY-X-N-X, whereas the SH2 domains in phosphatidylinositol 3-kinase (PI3K) recognize pY-X-X-M. Binding of the pY site in CD28 (pY-M-N-M) by PI3K and Grb2 through their SH2 domains is a key step that triggers the CD28 signal transduction for T cell activation and differentiation. In this study, we determined the crystal structure of the Grb2 SH2 domain in complex with a pY-containing peptide derived from CD28 at 1.35 Å resolution. The peptide was found to adopt a twisted U-type conformation, similar to, but distinct from type-I β-turn. In all previously reported crystal structures, the peptide bound to the Grb2 SH2 domains adopts a type-I β-turn conformation, except those with a proline residue at the pY+3 position. Molecular modeling also suggests that the same peptide bound to PI3K might adopt a very different conformation.

    Organizational Affiliation: 

    Research Institute for Biomedical Sciences, Tokyo University of Science, Noda-shi, Chiba, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Growth factor receptor-bound protein 2A98Homo sapiensMutation(s): 0 
Gene Names: GRB2, ASH
Find proteins for P62993 (Homo sapiens)
Explore P62993 
Go to UniProtKB:  P62993
NIH Common Fund Data Resources
PHAROS  P62993
GTEx  ENSG00000177885
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell-specific surface glycoprotein CD28B8Homo sapiensMutation(s): 0 
Gene Names: CD28
Find proteins for P10747 (Homo sapiens)
Explore P10747 
Go to UniProtKB:  P10747
NIH Common Fund Data Resources
PHAROS  P10747
GTEx  ENSG00000178562
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.01α = 90
b = 59.01β = 90
c = 117.09γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release