Crystal Structure of Dok1 PTB Domain

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.223 

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Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain

Shi, N.Ye, S.Bartlam, M.Yang, M.Wu, J.Liu, Y.Sun, F.Han, X.Peng, X.Qiang, B.Yuan, J.Rao, Z.

(2004) J Biol Chem 279: 4962-4969

  • DOI: https://doi.org/10.1074/jbc.M311030200
  • Primary Citation of Related Structures:  
    1P5T, 1UEF

  • PubMed Abstract: 

    Dok1 is a common substrate of activated protein-tyrosine kinases. It is rapidly tyrosine-phosphorylated in response to receptor tyrosine activation and interacts with ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathway activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively. In chronic myelogenous leukemia cells, it has shown constitutive phosphorylation. The N-terminal phosphotyrosine binding (PTB) domain of Dok1 can recognize and bind specifically to phosphotyrosine-containing motifs of receptors. Here we report the crystal structure of the Dok1 PTB domain alone and in complex with a phosphopeptide derived from RET receptor tyrosine kinase. The structure consists of a beta-sandwich composed of two nearly orthogonal, 7-stranded, antiparallel beta-sheets, and it is capped at one side by a C-terminal alpha-helix. The RET phosphopeptide binds to Dok1 via a surface groove formed between strand beta5 and the C-terminal alpha-helix of the PTB domain. The structures reveal the molecular basis for the specific recognition of RET by the Dok1 PTB domain. We also show that Dok1 does not recognize peptide sequences from TrkA and IL-4, which are recognized by Shc and IRS1, respectively.

  • Organizational Affiliation

    Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100084, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Docking protein 1
A, B
127Mus musculusMutation(s): 1 
Gene Names: mdok1
Find proteins for P97465 (Mus musculus)
Explore P97465 
Go to UniProtKB:  P97465
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97465
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.11α = 90
b = 56.25β = 90
c = 99.79γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
RESOLVEmodel building
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance