2WUH | pdb_00002wuh

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

• PDB DOI: https://doi.org/10.2210/pdb2WUH/pdb

• Classification: RECEPTOR/PEPTIDE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2009-10-05 Released: 2009-12-29 
• Deposition Author(s): Carafoli, F., Bihan, D., Stathopoulos, S., Konitsiotis, A.D., Kvansakul, M., Farndale, R.W., Leitinger, B., Hohenester, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Models: experimental

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

• PubMed: 20004161 
• DOI: https://doi.org/10.1016/j.str.2009.10.012
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
Division of National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK.
Department of Life Sciences, Imperial College London, London SW7 2AZ, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.01 kDa 
• Atom Count: 2,021 
• Modeled Residue Count: 249 
• Deposited Residue Count: 265 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DISCOIDIN DOMAIN RECEPTOR 2	A	178	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000162733

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COLLAGEN PEPTIDE	B, C, D	29	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	B, C, D	L-PEPTIDE LINKING	C5 H9 N O3		PRO
NLE	B, C, D	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.397	α = 66.19
b = 40.863	β = 88.9
c = 48.917	γ = 76.92

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Carafoli, F., Bihan, D., Stathopoulos, S., Konitsiotis, A.D., Kvansakul, M., Farndale, R.W., Leitinger, B., Hohenester, E.

Revision History  

• 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
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description