2WUH

Crystal structure of the DDR2 discoidin domain bound to a triple- helical collagen peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic Insight Into Collagen Recognition by Discoidin Domain Receptor 2

Carafoli, F.Bihan, D.Stathopoulos, S.Konitsiotis, A.D.Kvansakul, M.Farndale, R.W.Leitinger, B.Hohenester, E.

(2009) Structure 17: 1573

  • DOI: 10.1016/j.str.2009.10.012

  • PubMed Abstract: 
  • The discoidin domain receptors, DDR1 and DDR2, are widely expressed receptor tyrosine kinases that are activated by triple-helical collagen. They control important aspects of cell behavior and are dysregulated in several human diseases. The major DDR ...

    The discoidin domain receptors, DDR1 and DDR2, are widely expressed receptor tyrosine kinases that are activated by triple-helical collagen. They control important aspects of cell behavior and are dysregulated in several human diseases. The major DDR2-binding site in collagens I-III is a GVMGFO motif (O is hydroxyproline) that also binds the matricellular protein SPARC. We have determined the crystal structure of the discoidin domain of human DDR2 bound to a triple-helical collagen peptide. The GVMGFO motifs of two collagen chains are recognized by an amphiphilic pocket delimited by a functionally critical tryptophan residue and a buried salt bridge. Collagen binding results in structural changes of DDR2 surface loops that may be linked to the process of receptor activation. A comparison of the GVMGFO-binding sites of DDR2 and SPARC reveals a striking case of convergent evolution in collagen recognition.


    Related Citations: 
    • Characterization of High Affinity Binding Motifs for the Discoidin Domain Receptor Ddr2 in Collagen.
      Konitsiotis, A.D.,Raynal, N.,Bihan, D.,Hohenester, E.,Farndale, R.W.,Leitinger, B.
      (2008) J.Biol.Chem. 283: 6861
    • Structural Basis of the Collagen-Binding Mode of Discoidin Domain Receptor 2.
      Ichikawa, O.,Osawa, M.,Nishida, N.,Goshima, N.,Nomura, N.,Shimada, I.
      (2007) Embo J. 26: 4168


    Organizational Affiliation

    Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DISCOIDIN DOMAIN RECEPTOR 2
A
178Homo sapiensMutation(s): 0 
Gene Names: DDR2 (NTRKR3, TKT, TYRO10)
EC: 2.7.10.1
Find proteins for Q16832 (Homo sapiens)
Go to Gene View: DDR2
Go to UniProtKB:  Q16832
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COLLAGEN PEPTIDE
B, C, D
29N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
B, C, D
L-PEPTIDE LINKINGC5 H9 N O3PRO
NLE
Query on NLE
B, C, D
L-PEPTIDE LINKINGC6 H13 N O2LEU
ACE
Query on ACE
B, C, D
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.397α = 66.19
b = 40.863β = 88.90
c = 48.917γ = 76.92
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance