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PDBsum entry 1m3d
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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
1m3d

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
(+ 2 more) 223 a.a. *
222 a.a. *
Ligands
GOL ×8
Metals
_BR ×36
_LU ×4
Waters ×1138
* Residue conservation analysis
PDB id:
1m3d
Name: Structural protein
Title: Structure of type iv collagen nc1 domains
Structure: Type iv collagen noncollagenous domain- alpha1. Chain: a, b, d, e, g, h, j, k. Fragment: nc1 domain (residues 1-229). Type iv collagen noncollagenous domain- alpha2. Chain: c, f, i, l. Fragment: nc1 domain (residues 1-227)
Source: Bos taurus. Cattle. Organism_taxid: 9913. Other_details: bovine eye lens capsule. Other_details: bovine eye lens capsule
Biol. unit: Hexamer (from PQS)
Resolution:
2.00Å     R-factor:   0.169     R-free:   0.197
Authors: M.Sundaramoorthy,M.Meiyappan,P.Todd,B.G.Hudson
Key ref:
M.Sundaramoorthy et al. (2002). Crystal structure of NC1 domains. Structural basis for type IV collagen assembly in basement membranes. J Biol Chem, 277, 31142-31153. PubMed id: 11970952 DOI: 10.1074/jbc.M201740200
Date:
27-Jun-02     Release date:   07-Jan-03    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7SIB2  (CO4A1_BOVIN) -  Collagen alpha-1(IV) chain from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1669 a.a.
223 a.a.
Protein chains
Pfam   ArchSchema ?
Q7SIB3  (CO4A2_BOVIN) -  Collagen alpha-2(IV) chain (Fragment) from Bos taurus
Seq:
Struc: 		227 a.a.
222 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1074/jbc.M201740200 J Biol Chem 277:31142-31153 (2002)
PubMed id: 11970952  
 
 
Crystal structure of NC1 domains. Structural basis for type IV collagen assembly in basement membranes.
M.Sundaramoorthy, M.Meiyappan, P.Todd, B.G.Hudson.
 
  ABSTRACT  
 
Type IV collagen, which is present in all metazoan, exists as a family of six homologous alpha(IV) chains, alpha1-alpha6, in mammals. The six chains assemble into three different triple helical protomers and self-associate as three distinct networks. The network underlies all epithelia as a component of basement membranes, which play important roles in cell adhesion, growth, differentiation, tissue repair and molecular ultrafiltration. The specificity of both protomer and network assembly is governed by amino acid sequences of the C-terminal noncollagenous (NC1) domain of each chain. In this study, the structural basis for protomer and network assembly was investigated by determining the crystal structure of the ubiquitous [(alpha1)(2).alpha2](2) NC1 hexamer of bovine lens capsule basement membrane at 2.0 A resolution. The NC1 monomer folds into a novel tertiary structure. The (alpha1)(2).alpha2 trimer is organized through the unique three-dimensional domain swapping interactions. The differences in the primary sequences of the hypervariable region manifest in different secondary structures, which determine the chain specificity at the monomer-monomer interfaces. The trimer-trimer interface is stabilized by the extensive hydrophobic and hydrophilic interactions without a need for disulfide cross-linking.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Stereo view of a section of 2Fo F[c] map (contoured at 1 ), where differences between the human and bovine sequences occur ( 2: D96E and E97D) (refer also to Fig. 2 legend). 		Figure 8.
Fig. 8. Comparison of the essential hydrogen bonding interactions in the interface at the "core" (A) and the "outer" (B) and major-minor junctions (C) for 1- 1 and 1- 2 dimers at the trimer-trimer interface (see text for details).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 31142-31153) copyright 2002.  
  Figures were 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
21447121 R.Vanacore, V.Pedchenko, G.Bhave, and B.G.Hudson (2011).
Sulphilimine cross-links in Goodpasture's disease.
  Clin Exp Immunol, 164, 4-6.  
21378566 V.Pedchenko, R.Vanacore, and B.Hudson (2011).
Goodpasture's disease: molecular architecture of the autoantigen provides clues to etiology and pathogenesis.
  Curr Opin Nephrol Hypertens, 20, 290-296.  
19634988 M.A.Wouters, S.W.Fan, and N.L.Haworth (2010).
Disulfides as redox switches: from molecular mechanisms to functional significance.
  Antioxid Redox Signal, 12, 53-91.  
20815642 T.A.Powell, R.Amini, A.Oltean, V.A.Barnett, K.D.Dorfman, Y.Segal, and V.H.Barocas (2010).
Elasticity of the porcine lens capsule as measured by osmotic swelling.
  J Biomech Eng, 132, 091008.  
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.  
19729652 R.Vanacore, A.J.Ham, M.Voehler, C.R.Sanders, T.P.Conrads, T.D.Veenstra, K.B.Sharpless, P.E.Dawson, and B.G.Hudson (2009).
A sulfilimine bond identified in collagen IV.
  Science, 325, 1230-1234.  
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
18219669 J.Khoshnoodi, V.Pedchenko, and B.G.Hudson (2008).
Mammalian collagen IV.
  Microsc Res Tech, 71, 357-370.  
18930919 J.S.Kang, S.Colon, T.Hellmark, Y.Sado, B.G.Hudson, and D.B.Borza (2008).
Identification of noncollagenous sites encoding specific interactions and quaternary assembly of alpha 3 alpha 4 alpha 5(IV) collagen: implications for Alport gene therapy.
  J Biol Chem, 283, 35070-35077.  
18499662 R.M.Vanacore, A.J.Ham, J.P.Cartailler, M.Sundaramoorthy, P.Todd, V.Pedchenko, Y.Sado, D.B.Borza, and B.G.Hudson (2008).
A role for collagen IV cross-links in conferring immune privilege to the Goodpasture autoantigen: structural basis for the crypticity of B cell epitopes.
  J Biol Chem, 283, 22737-22748.  
18973809 Y.J.Chen, and M.Inouye (2008).
The intramolecular chaperone-mediated protein folding.
  Curr Opin Struct Biol, 18, 765-770.  
16915401 G.Coleman, T.A.Gardiner, A.Boutaud, and A.W.Stitt (2007).
Recombinant alpha2(IV)NC1 domain of type IV collagen is an effective regulator of retinal capillary endothelial cell proliferation and inhibits pre-retinal neovascularisation.
  Graefes Arch Clin Exp Ophthalmol, 245, 581-587.  
17179069 J.Favor, C.J.Gloeckner, D.Janik, M.Klempt, A.Neuhäuser-Klaus, W.Pretsch, W.Schmahl, and L.Quintanilla-Fend (2007).
Type IV procollagen missense mutations associated with defects of the eye, vascular stability, the brain, kidney function and embryonic or postnatal viability in the mouse, Mus musculus: an extension of the Col4a1 allelic series and the identification of the first two Col4a2 mutant alleles.
  Genetics, 175, 725-736.  
17133346 P.A.Campochiaro (2007).
Molecular targets for retinal vascular diseases.
  J Cell Physiol, 210, 575-581.  
16579685 B.Brown, K.Lindberg, J.Reing, D.B.Stolz, and S.F.Badylak (2006).
The basement membrane component of biologic scaffolds derived from extracellular matrix.
  Tissue Eng, 12, 519-526.  
17043797 C.Petibois, G.Gouspillou, K.Wehbe, J.P.Delage, and G.Déléris (2006).
Analysis of type I and IV collagens by FT-IR spectroscopy and imaging for a molecular investigation of skeletal muscle connective tissue.
  Anal Bioanal Chem, 386, 1961-1966.  
16534749 J.J.Calvete, F.Revert, M.Blanco, J.Cervera, C.Tárrega, L.Sanz, F.Revert-Ros, F.Granero, E.Pérez-Payá, B.G.Hudson, and J.Saus (2006).
Conformational diversity of the Goodpasture antigen, the noncollagenous-1 domain of the alpha3 chain of collagen IV.
  Proteomics, 6, S237-S244.  
16557520 R.Lima E Silva, S.Kachi, H.Akiyama, J.Shen, S.Aslam, Y.Yuan Gong, N.H.Khu, M.C.Hatara, A.Boutaud, R.Peterson, and P.A.Campochiaro (2006).
Recombinant non-collagenous domain of alpha2(IV) collagen causes involution of choroidal neovascularization by inducing apoptosis.
  J Cell Physiol, 208, 161-166.  
16865710 T.J.Molloy, C.E.de Bock, Y.Wang, and G.A.Murrell (2006).
Gene expression changes in SNAP-stimulated and iNOS-transfected tenocytes--expression of extracellular matrix genes and its implications for tendon-healing.
  J Orthop Res, 24, 1869-1882.  
  15743801 J.M.Roth, A.Akalu, A.Zelmanovich, D.Policarpio, B.Ng, S.MacDonald, S.Formenti, L.Liebes, and P.C.Brooks (2005).
Recombinant alpha2(IV)NC1 domain inhibits tumor cell-extracellular matrix interactions, induces cellular senescence, and inhibits tumor growth in vivo.
  Am J Pathol, 166, 901-911.  
16201871 M.E.Than, G.P.Bourenkov, S.Henrich, K.Mann, and W.Bode (2005).
The NC1 dimer of human placental basement membrane collagen IV: does a covalent crosslink exist?
  Biol Chem, 386, 759-766.  
  14582039 B.Tazón Vega, C.Badenas, E.Ars, X.Lens, M.Milà, A.Darnell, and R.Torra (2003).
Autosomal recessive Alport's syndrome and benign familial hematuria are collagen type IV diseases.
  Am J Kidney Dis, 42, 952-959.  
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
12778132 R.Kalluri (2003).
Basement membranes: structure, assembly and role in tumour angiogenesis.
  Nat Rev Cancer, 3, 422-433.  
12376553 N.Ortega, and Z.Werb (2002).
New functional roles for non-collagenous domains of basement membrane collagens.
  J Cell Sci, 115, 4201-4214.  
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.

 

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