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Collagen PDB id
1gr3
Jmol
Contents
Protein chain
132 a.a. *
Ligands
CPS
Metals
_CA ×2
_NA
Waters ×40
* Residue conservation analysis
PDB id:
1gr3
Name: Collagen
Title: Structure of the human collagen x nc1 trimer
Structure: Collagen x. Chain: a. Fragment: nc1 domain, residues 521-680. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
2.0Å     R-factor:   0.186     R-free:   0.199
Authors: O.Bogin,M.Kvansakul,E.Rom,J.Singer,A.Yayon,E.Hohenester
Key ref:
O.Bogin et al. (2002). Insight into Schmid metaphyseal chondrodysplasia from the crystal structure of the collagen X NC1 domain trimer. Structure, 10, 165-173. PubMed id: 11839302 DOI: 10.1016/S0969-2126(02)00697-4
Date:
12-Dec-01     Release date:   14-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q03692  (COAA1_HUMAN) -  Collagen alpha-1(X) chain
Seq:
Struc: 		 
Seq:
Struc: 		680 a.a.
132 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0969-2126(02)00697-4 Structure 10:165-173 (2002)
PubMed id: 11839302  
 
 
Insight into Schmid metaphyseal chondrodysplasia from the crystal structure of the collagen X NC1 domain trimer.
O.Bogin, M.Kvansakul, E.Rom, J.Singer, A.Yayon, E.Hohenester.
 
  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.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Location of SMCD Missense MutationsStereoview of a Ca trace of the collagen X NC1 trimer, with one subunit in pink and the other subunits in dark blue. Side chains of residues mutated in SMCD (see text) are shown as ball and stick models in the pink subunit and are labeled.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 165-173) copyright 2002.  
  Figure was selected by an automated process.  

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
20872587 O.Mäkitie, M.Susic, and W.G.Cole (2010).
Early-onset metaphyseal chondrodysplasia type Schmid associated with a COL10A1 frame-shift mutation and impaired trimerization of wild-type α1(X) protein chains.
  J Orthop Res, 28, 1497-1501.  
19851784 R.P.Boot-Handford, and M.D.Briggs (2010).
The unfolded protein response and its relevance to connective tissue diseases.
  Cell Tissue Res, 339, 197-211.  
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
19204719 J.F.Bateman, R.P.Boot-Handford, and S.R.Lamandé (2009).
Genetic diseases of connective tissues: cellular and extracellular effects of ECM mutations.
  Nat Rev Genet, 10, 173-183.  
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.  
17331201 T.Iijima, E.Miura, K.Matsuda, Y.Kamekawa, M.Watanabe, and M.Yuzaki (2007).
Characterization of a transneuronal cytokine family Cbln--regulation of secretion by heteromeric assembly.
  Eur J Neurosci, 25, 1049-1057.  
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.  
15880705 J.F.Bateman, R.Wilson, S.Freddi, S.R.Lamandé, and R.Savarirayan (2005).
Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia.
  Hum Mutat, 25, 525-534.  
16088909 O.Mäkitie, M.Susic, L.Ward, C.Barclay, F.H.Glorieux, and W.G.Cole (2005).
Schmid type of metaphyseal chondrodysplasia and COL10A1 mutations--findings in 10 patients.
  Am J Med Genet A, 137, 241-248.  
15695517 R.Wilson, S.Freddi, D.Chan, K.S.Cheah, and J.F.Bateman (2005).
Misfolding of collagen X chains harboring Schmid metaphyseal chondrodysplasia mutations results in aberrant disulfide bond formation, intracellular retention, and activation of the unfolded protein response.
  J Biol Chem, 280, 15544-15552.  
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.  
12595739 A.L.Gall, M.Ruff, and D.Moras (2003).
The dual role of CHAPS in the crystallization of stromelysin-3 catalytic domain.
  Acta Crystallogr D Biol Crystallogr, 59, 603-606.  
12920133 A.McAlinden, T.A.Smith, L.J.Sandell, D.Ficheux, D.A.Parry, and D.J.Hulmes (2003).
Alpha-helical coiled-coil oligomerization domains are almost ubiquitous in the collagen superfamily.
  J Biol Chem, 278, 42200-42207.  
12960167 C.Gaboriaud, J.Juanhuix, A.Gruez, M.Lacroix, C.Darnault, D.Pignol, D.Verger, J.C.Fontecilla-Camps, and G.J.Arlaud (2003).
The crystal structure of the globular head of complement protein C1q provides a basis for its versatile recognition properties.
  J Biol Chem, 278, 46974-46982.
PDB code: 1pk6
  12623021 J.Stetefeld, S.Frank, M.Jenny, T.Schulthess, R.A.Kammerer, S.Boudko, R.Landwehr, K.Okuyama, and J.Engel (2003).
Collagen stabilization at atomic level: crystal structure of designed (GlyProPro)10foldon.
  Structure, 11, 339-346.
PDB code: 1nay
  14656435 S.G.Hymowitz, D.M.Compaan, M.Yan, H.J.Wallweber, V.M.Dixit, M.A.Starovasnik, and A.M.de Vos (2003).
The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity.
  Structure, 11, 1513-1520.
PDB code: 1rj8
11970952 M.Sundaramoorthy, M.Meiyappan, P.Todd, and B.G.Hudson (2002).
Crystal structure of NC1 domains. Structural basis for type IV collagen assembly in basement membranes.
  J Biol Chem, 277, 31142-31153.
PDB code: 1m3d
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.