N-terminal NC4 domain of collagen IX

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

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Crystal Structure of the N-Terminal Nc4 Domain of Collagen Ix, a Zinc Binding Member of the Laminin-Neurexin-Sex Hormone Binding Globulin (Lns) Domain Family.

Leppanen, V.-M.Tossavainen, H.Permi, P.Lehtio, L.Ronnholm, G.Goldman, A.Kilpelainen, I.Pihlajamaa, T.

(2007) J Biol Chem 282: 23219

  • DOI: https://doi.org/10.1074/jbc.M702514200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Collagen IX, located on the surface of collagen fibrils, is crucial for cartilage integrity and stability. The N-terminal NC4 domain of the alpha1(IX) chain is probably important in this because it interacts with various macromolecules such as proteoglycans and cartilage oligomeric matrix protein. At least 17 distinct collagen polypeptides carry an NC4-like unit near their N terminus, but this report, describing the crystal structure of NC4 at 1.8-A resolution, represents the first atomic level structure for these domains. The structure is similar to previously characterized laminin-neurexin-sex hormone binding globulin (LNS) structures, dominated by an antiparallel beta-sheet sandwich. In addition, a zinc ion was found in a position similar to that of the metal binding site of other LNS domains. A partial backbone NMR assignment of NC4 was obtained and utilized in NMR titration studies to investigate the zinc binding in solution state and to quantitate the affinity of metal binding. The K(d) of 11.5 mM suggests a regulatory rather than a structural role for zinc in solution. NMR titration with a heparin tetrasaccharide revealed the presence of a secondary binding site for heparin on NC4, showing structural and functional conservation with thrombospondin-1, but a markedly reduced affinity for the ligand. Also the overall arrangement of the N and C termini of NC4 resembles most closely the N-terminal domain of thrombospondin-1, distinguishing the two from the majority of the published LNS structures.

  • Organizational Affiliation

    Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COLLAGEN ALPHA-1(IX) CHAIN245Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20849 (Homo sapiens)
Explore P20849 
Go to UniProtKB:  P20849
PHAROS:  P20849
GTEx:  ENSG00000112280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20849
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.888α = 90
b = 81.888β = 90
c = 71.429γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance