1GR3

Structure of the human collagen X NC1 trimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Insight Into Schmid Metaphyseal Chondrodysplasia from the Crystal Structure of the Collagen X Nc1 Domain Trimer.

Bogin, O.Kvansakul, M.Rom, E.Singer, J.Yayon, A.Hohenester, E.

(2002) Structure 10: 165

  • DOI: https://doi.org/10.1016/s0969-2126(02)00697-4
  • Primary Citation of Related Structures:  
    1GR3

  • PubMed Abstract: 

    Collagen X is expressed specifically in the growth plate of long bones. Its C1q-like C-terminal NC1 domain forms a stable homotrimer and is crucial for collagen X assembly. Mutations in the NC1 domain cause Schmid metaphyseal chondrodysplasia (SMCD). The crystal structure at 2.0 A resolution of the human collagen X NC1 domain reveals an intimate trimeric assembly strengthened by a buried cluster of calcium ions. Three strips of exposed aromatic residues on the surface of NC1 trimer are likely to be involved in the supramolecular assembly of collagen X. Most internal SMCD mutations probably prevent protein folding, whereas mutations of surface residues may affect the collagen X suprastructure in a dominant-negative manner.


  • Organizational Affiliation

    ProChon Biotech, P.O. Box 1482, Rehovot 76114, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COLLAGEN X160Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03692 (Homo sapiens)
Explore Q03692 
Go to UniProtKB:  Q03692
PHAROS:  Q03692
GTEx:  ENSG00000123500 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03692
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.36α = 90
b = 78.36β = 90
c = 141.036γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-14
    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: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description