Crystal structure of a collagen II fragment containing the binding site of PEDF and COMP, (POG)4-LKG HRG FTG LQG-POG(4)

Experimental Data Snapshot

  • Resolution: 1.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

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COMP and TSP-4 interact specifically with the novel GXKGHR motif only found in fibrillar collagens.

Gebauer, J.M.Kohler, A.Dietmar, H.Gompert, M.Neundorf, I.Zaucke, F.Koch, M.Baumann, U.

(2018) Sci Rep 8: 17187-17187

  • DOI: https://doi.org/10.1038/s41598-018-35447-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    COMP (cartilage oligomeric matrix protein) is a member of the thrombospondin family and forms homopentamers as well as mixed heterooligomers with its closely related family member TSP-4. COMP is long known to bind to collagens and to influence collagen fibril formation. Recent work indicates that already intracellular interaction with collagen is important for collagen secretion. However, the exact binding site of COMP on the collagen triple helix has not been described up to now. In this study we have identified a GXKGHR motif on the collagen II helix to bind to COMP, using a recombinantly expressed collagen II peptide library. This binding sequence is conserved throughout evolution and we demonstrate that TSP-4 binds to the same sequence. The identified binding motif overlaps with the recognition sites of many other collagen-binding partners (e.g. PEDF, Heparin) and also spans the lysine residues, which form collagen cross-links. COMP might thereby protect collagen helices from premature modification and cross-linking. Interestingly, this motif is only found in classical fibrillar collagens, although COMP is known to also bind other types. This might indicate that COMP has a unique interface for fibrillar collagens, thus making it an interesting target for the development of antifibrotic drugs.

  • Organizational Affiliation

    Institute of Biochemistry, University of Cologne, Cologne, Germany. jan.gebauer@uni-koeln.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-1(II) chain
A, B, C
38Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02458 (Homo sapiens)
Explore P02458 
Go to UniProtKB:  P02458
PHAROS:  P02458
GTEx:  ENSG00000139219 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02458
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on HYP
A, B, C
Experimental Data & Validation

Experimental Data

  • Resolution: 1.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.97α = 90
b = 23.64β = 92.702
c = 107.939γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB829/B11

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 2.0: 2019-06-19
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-10-16
    Changes: Data collection
  • Version 2.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description