2WUH

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

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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
  • Primary Citation of Related Structures:  
    2WUH

  • 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 DDR2-binding site in collagens I-III is a GVMGFO motif (O is hydroxyproline) that also binds the matricellular protein SPARC ...

    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: 
    • 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
    • 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
    Organizational Affiliation: 

    Department of Life Sciences, Imperial College London, London SW7 2AZ, UK. Electronic address: e.hohenester@imperial.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DISCOIDIN DOMAIN RECEPTOR 2A178Homo sapiensMutation(s): 0 
Gene Names: DDR2, NTRKR3, TKT, TYRO10
EC: 2.7.10.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16832 (Homo sapiens)
Explore Q16832 
Go to UniProtKB:  Q16832
PHAROS:  Q16832
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16832
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COLLAGEN PEPTIDEB, C, D29Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.397α = 66.19
b = 40.863β = 88.9
c = 48.917γ = 76.92
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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