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Collagen PDB id
1o91
Jmol
Contents
Protein chains
131 a.a. *
Ligands
CPS
SO4
Waters ×268
* Residue conservation analysis
PDB id:
1o91
Name: Collagen
Title: Crystal structure of a collagen viii nc1 domain trimer
Structure: Collagen alpha 1(viii) chain. Chain: a, b, c. Fragment: nonhelical region (nc1), residues 613-743. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
1.9Å     R-factor:   0.185     R-free:   0.209
Authors: M.Kvansakul,O.Bogin,E.Hohenester,A.Yayon
Key ref: M.Kvansakul et al. (2003). Crystal structure of the collagen alpha1(VIII) NC1 trimer. Matrix Biol, 22, 145-152. PubMed id: 12782141 DOI: 10.1016/S0945-053X(02)00119-1
Date:
10-Dec-02     Release date:   20-Nov-03    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q00780  (CO8A1_MOUSE) -  Collagen alpha-1(VIII) chain
Seq:
Struc: 		 
Seq:
Struc: 		744 a.a.
131 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0945-053X(02)00119-1 Matrix Biol 22:145-152 (2003)
PubMed id: 12782141  
 
 
Crystal structure of the collagen alpha1(VIII) NC1 trimer.
M.Kvansakul, O.Bogin, E.Hohenester, A.Yayon.
 
  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 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20932905 J.A.Wirz, S.P.Boudko, T.F.Lerch, M.S.Chapman, and H.P.Bächinger (2011).
Crystal structure of the human collagen XV trimerization domain: a potent trimerizing unit common to multiplexin collagens.
  Matrix Biol, 30, 9.
PDB code: 3n3f
19996152 C.Shimono, R.Manabe, T.Yamada, S.Fukuda, J.Kawai, Y.Furutani, K.Tsutsui, K.Ikenaka, Y.Hayashizaki, and K.Sekiguchi (2010).
Identification and characterization of nCLP2, a novel C1q family protein expressed in the central nervous system.
  J Biochem, 147, 565-579.  
20162611 Z.Yu, O.Mirochnitchenko, C.Xu, A.Yoshizumi, B.Brodsky, and M.Inouye (2010).
Noncollagenous region of the streptococcal collagen-like protein is a trimerization domain that supports refolding of adjacent homologous and heterologous collagenous domains.
  Protein Sci, 19, 775-785.  
19023665 G.Verdone, A.Corazza, S.A.Colebrooke, D.Cicero, T.Eliseo, J.Boyd, R.Doliana, F.Fogolari, P.Viglino, A.Colombatti, I.D.Campbell, and G.Esposito (2009).
NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1.
  J Biomol NMR, 43, 79-96.
PDB code: 2ka3
19631658 S.P.Boudko, T.Sasaki, J.Engel, T.F.Lerch, J.Nix, M.S.Chapman, and H.P.Bächinger (2009).
Crystal structure of human collagen XVIII trimerization domain: A novel collagen trimerization Fold.
  J Mol Biol, 392, 787-802.
PDB codes: 3hon 3hsh
18463100 G.Verdone, R.Doliana, A.Corazza, S.A.Colebrooke, P.Spessotto, S.Bot, F.Bucciotti, A.Capuano, A.Silvestri, P.Viglino, I.D.Campbell, A.Colombatti, and G.Esposito (2008).
The solution structure of EMILIN1 globular C1q domain reveals a disordered insertion necessary for interaction with the alpha4beta1 integrin.
  J Biol Chem, 283, 18947-18956.  
19035365 J.M.Gansner, and J.D.Gitlin (2008).
Essential role for the alpha 1 chain of type VIII collagen in zebrafish notochord formation.
  Dev Dyn, 237, 3715-3726.  
16905106 D.M.Compaan, and S.G.Hymowitz (2006).
The crystal structure of the costimulatory OX40-OX40L complex.
  Structure, 14, 1321-1330.
PDB codes: 2hev 2hew 2hey
17082192 J.Khoshnoodi, J.P.Cartailler, K.Alvares, A.Veis, and B.G.Hudson (2006).
Molecular recognition in the assembly of collagens: terminal noncollagenous domains are key recognition modules in the formation of triple helical protomers.
  J Biol Chem, 281, 38117-38121.  
16135095 D.Bao, Z.Pang, and J.I.Morgan (2005).
The structure and proteolytic processing of Cbln1 complexes.
  J Neurochem, 95, 618-629.  
16249180 S.Réty, S.Salamitou, I.Garcia-Verdugo, D.J.Hulmes, F.Le Hégarat, R.Chaby, and A.Lewit-Bentley (2005).
The crystal structure of the Bacillus anthracis spore surface protein BclA shows remarkable similarity to mammalian proteins.
  J Biol Chem, 280, 43073-43078.
PDB code: 1wck
15735346 S.Salamitou, S.Réty, F.Le Hégarat, G.Leblon, and A.Lewit-Bentley (2005).
The use of high halide-ion concentrations and automated phasing procedures for the structural analysis of BclA, the major component of the exosporium of Bacillus anthracis spores.
  Acta Crystallogr D Biol Crystallogr, 61, 344-349.  
14990571 S.Stephan, M.J.Sherratt, N.Hodson, C.A.Shuttleworth, and C.M.Kielty (2004).
Expression and supramolecular assembly of recombinant alpha1(viii) and alpha2(viii) collagen homotrimers.
  J Biol Chem, 279, 21469-21477.  
15364058 U.Kishore, C.Gaboriaud, P.Waters, A.K.Shrive, T.J.Greenhough, K.B.Reid, R.B.Sim, and G.J.Arlaud (2004).
C1q and tumor necrosis factor superfamily: modularity and versatility.
  Trends Immunol, 25, 551-561.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.