Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report

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Molecular basis for regulation of Src by the docking protein p130Cas

Nasertorabi, F.Tars, K.Becherer, K.Kodandapani, R.Liljas, L.Vuori, K.Ely, K.R.

(2006) J Mol Recognit 19: 30-38

  • DOI: https://doi.org/10.1002/jmr.755
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The docking protein p130Cas (Cas) becomes tyrosine-phosphorylated in its central substrate domain in response to extracellular stimuli such as integrin-mediated cell adhesion, and transmits signals through interactions with various intracellular signaling molecules such as the adaptor protein Crk. Src-family kinases (SFKs) bind a specific site in the carboxyl-terminal region of Cas and subsequently SFKs phosphorylate progressively the substrate domain in Cas. In this study crystallography, mutagenesis and binding assays were used to understand the molecular basis for Cas interactions with SFKs. Tyrosine phosphorylation regulates binding of Cas to SFKs, and the primary site for this phosphorylation, Y762, has been proposed. A phosphorylated peptide corresponding to Cas residues 759MEDpYDYVHL767 containing the key phosphotyrosine was crystallized in complex with the SH3-SH2 domain of the SFK Lck. The results provide the first structural data for this protein-protein interaction. The motif in Cas 762pYDYV binds to the SH2 domain in a mode that mimics high-affinity ligands, involving dual contacts of Y762 and V765 with conserved residues in SFK SH2 domains. In addition, Y764 is in position to make an electrostatic contact after phosphorylation with a conserved SFK arginine that mediates interactions with other high-affinity SH2 binders. These new molecular data suggest that Cas may regulate activity of Src as a competing ligand to displace intramolecular interactions that occur in SFKs (between the C-terminal tail and the SH2 domain) and restrain and down-regulate the kinase in an inactive form.

  • Organizational Affiliation

    Cancer Center, The Burnham Institute for Medical Research, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase LCK
A, B, C, D, E
A, B, C, D, E, F
167Homo sapiensMutation(s): 0 
Gene Names: LCK
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens)
Explore P06239 
Go to UniProtKB:  P06239
PHAROS:  P06239
GTEx:  ENSG00000182866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06239
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRK-associated substrate9N/AMutation(s): 1 
Find proteins for Q63767 (Rattus norvegicus)
Explore Q63767 
Go to UniProtKB:  Q63767
Entity Groups  
UniProt GroupQ63767
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
G [auth I]
H [auth J]
I [auth K]
J [auth L]
K [auth M]
G [auth I],
H [auth J],
I [auth K],
J [auth L],
K [auth M],
L [auth N]
Binding Affinity Annotations 
IDSourceBinding Affinity
PTR BindingDB:  1X27 Kd: 4.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.415α = 90
b = 107.289β = 90
c = 166.389γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection