1O91

Crystal Structure of a Collagen VIII NC1 Domain Trimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Collagen Alpha1(Viii) Nc1 Trimer.

Kvansakul, M.Bogin, O.Hohenester, E.Yayon, A.

(2003) Matrix Biol. 22: 145


  • PubMed Abstract: 
  • Collagen VIII is a major component of Descemet's membrane and is also found in vascular subendothelial matrices. The C-terminal non-collagenous domain (NC1) domain of collagen VIII, which is a member of the C1q-like protein family, forms a stable tri ...

    Collagen VIII is a major component of Descemet's membrane and is also found in vascular subendothelial matrices. The C-terminal non-collagenous domain (NC1) domain of collagen VIII, which is a member of the C1q-like protein family, forms a stable trimer and is thought to direct the assembly of the collagen triple helix, as well as polygonal supramolecular structures. We have solved the crystal structure of the mouse alpha1(VIII)(3) NC1 domain trimer at 1.9 A resolution. Each subunit of the intimate NC1 trimer consists of a ten-stranded beta-sandwich. The surface of the collagen VIII NC1 trimer presents three strips of partially exposed aromatic residues shown to interact with the non-ionic detergent CHAPS, which are likely to be involved in supramolecular assemblies. Equivalent strips exist in the NC1 domain of the closely related collagen X, suggesting a conserved assembly mechanism. Surprisingly, the collagen VIII NC1 trimer lacks the buried calcium cluster of the collagen X NC1 trimer. The mouse alpha1(VIII) and alpha2(VIII) NC1 domains are 71.5% identical in sequence, with the differences being concentrated on the NC1 trimer surface. A few non-conservative substitutions map to the subunit interfaces near the surface, but it is not obvious from the structure to what extent they determine the preferred assembly of collagen VIII alpha1 and alpha2 chains into homotrimers.


    Related Citations: 
    • 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
    • Type Viii Collagen
      Shuttleworth, C.A.
      (1997) Int. J. Biochem. Cell Biol. 29: 1145


    Organizational Affiliation

    Department of Biological Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLLAGEN ALPHA 1(VIII) CHAIN
A, B, C
178Mus musculusGene Names: Col8a1
Find proteins for Q00780 (Mus musculus)
Go to UniProtKB:  Q00780
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CPS
Query on CPS

Download SDF File 
Download CCD File 
C
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
CHAPS
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.590α = 90.00
b = 82.550β = 90.00
c = 89.940γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-20
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2017-07-05
    Type: Data collection