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PDBsum entry 3ejh
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protein ligands Protein-protein interface(s) links
Cell adhesion PDB id
3ejh

 

 

 

 

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Contents
Protein chains
91 a.a. *
15 a.a. *
22 a.a. *
Ligands
NAG ×2
GOL
Waters ×105
* Residue conservation analysis
PDB id:
3ejh
Name: Cell adhesion
Title: Crystal structure of the fibronectin 8-9fni domain pair in complex with a type-i collagen peptide
Structure: Fibronectin. Chain: a, b. Fragment: 8-9fni. Synonym: fn,cold-insoluble globulin,cig. Engineered: yes. Mutation: yes. Collagen type-i a1 chain. Chain: e, f. Fragment: collagenase sitE C-terminal peptide.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: fn1, fn. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in homo sapiens (human) type-i
Resolution:
2.10Å     R-factor:   0.211     R-free:   0.242
Authors: M.C.Erat,E.D.Lowe,I.D.Campbell,I.Vakonakis
Key ref:
M.C.Erat et al. (2009). Identification and structural analysis of type I collagen sites in complex with fibronectin fragments. Proc Natl Acad Sci U S A, 106, 4195-4200. PubMed id: 19251642 DOI: 10.1073/pnas.0812516106
Date:
18-Sep-08     Release date:   03-Feb-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02751  (FINC_HUMAN) -  Fibronectin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2477 a.a.
91 a.a.*
Protein chain
Pfam   ArchSchema ?
P02452  (CO1A1_HUMAN) -  Collagen alpha-1(I) chain from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1464 a.a.
15 a.a.*
Protein chain
Pfam   ArchSchema ?
P02452  (CO1A1_HUMAN) -  Collagen alpha-1(I) chain from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1464 a.a.
22 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 

 
DOI no: 10.1073/pnas.0812516106 Proc Natl Acad Sci U S A 106:4195-4200 (2009)
PubMed id: 19251642  
 
 
Identification and structural analysis of type I collagen sites in complex with fibronectin fragments.
M.C.Erat, D.A.Slatter, E.D.Lowe, C.J.Millard, R.W.Farndale, I.D.Campbell, I.Vakonakis.
 
  ABSTRACT  
 
Collagen and fibronectin are major components of vertebrate extracellular matrices. Their association and distribution control the development and properties of diverse tissues, but thus far no structural information has been available for the complex formed. Here, we report binding of a peptide, derived from the alpha(1) chain of type I collagen, to the gelatin-binding domain of human fibronectin and present the crystal structure of this peptide in complex with the (8-9)FnI domain pair. Both gelatin-binding domain subfragments, (6)FnI(1-2)FnII(7)FnI and (8-9)FnI, bind the same specific sequence on D-period 4 of collagen I alpha(1), adjacent to the MMP-1 cleavage site. (8-9)FnI also binds the equivalent sequence of the alpha(2) chain. The collagen peptide adopts an antiparallel beta-strand conformation, similar to structures of proteins from pathogenic bacteria bound to FnI domains. Analysis of the type I collagen sequence suggests multiple putative fibronectin-binding sites compatible with our structural model. We demonstrate, by kinetic unfolding experiments, that the triple-helical collagen state is destabilized by (8-9)FnI. This finding suggests a role for fibronectin in collagen proteolysis and tissue remodeling.
 
  Selected figure(s)  
 
Figure 3.
Overview of the complex structure. (A) Schematic representation of the ^8–9FnI module pair in gold and the α[1](I) G[778]–G[799] peptide in cyan showing the antiparallel β-strand mode of binding. (B) Similar representation of ^2–3FnI (purple) in complex with a peptide (gold) from Staphylococcus aureus (21). Collagen and bacterial peptides adopt a similar model of binding to FnI domains. (C) Molecular surface area representation of ^8–9FnI colored by electrostatic potential and select collagen peptides residues involved in complex formation. 		Figure 4.
Details from the molecular interaction of the complex. (A) Hydrophobic interactions stabilizing the ^8–9FnI (gold)–peptide (blue) conformation involve W[553] stacking above the peptide (blue) plane and L[785] of α[1](I) contacting H[539] and F[569]. (B) Stereoview of the β-stranded portion of the collagen peptide. Two salt bridges to ^8–9FnI are formed at its C terminus (green dashed lines) as well as important hydrogen bonds among the residues shown. (C) Stereoview of the peptide N terminus interacting with ^9FnI, primarily through hydrogen bonds (red dashed lines).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20695902 B.Henderson, S.Nair, J.Pallas, and M.A.Williams (2011).
Fibronectin: a multidomain host adhesin targeted by bacterial fibronectin-binding proteins.
  FEMS Microbiol Rev, 35, 147-200.  
21182410 J.P.Orgel, J.D.San Antonio, and O.Antipova (2011).
Molecular and structural mapping of collagen fibril interactions.
  Connect Tissue Res, 52, 2.  
21211003 M.Ruehl, M.Muche, C.Freise, U.Erben, U.Neumann, D.Schuppan, Y.Popov, W.Dieterich, M.Zeitz, R.W.Farndale, and R.Somasundaram (2011).
Hydroxyproline-containing collagen analogs trigger the release and activation of collagen-sequestered proMMP-2 by competition with prodomain-derived peptide P33-42.
  Fibrogenesis Tissue Repair, 4, 1.  
20676409 J.A.Fallas, L.E.O'Leary, and J.D.Hartgerink (2010).
Synthetic collagen mimics: self-assembly of homotrimers, heterotrimers and higher order structures.
  Chem Soc Rev, 39, 3510-3527.  
20843804 K.E.Atkin, A.S.Brentnall, G.Harris, R.J.Bingham, M.C.Erat, C.J.Millard, U.Schwarz-Linek, D.Staunton, I.Vakonakis, I.D.Campbell, and J.R.Potts (2010).
The streptococcal binding site in the gelatin-binding domain of fibronectin is consistent with a non-linear arrangement of modules.
  J Biol Chem, 285, 36977-36983.  
20947497 L.M.Maurer, B.R.Tomasini-Johansson, W.Ma, D.S.Annis, N.L.Eickstaedt, M.G.Ensenberger, K.A.Satyshur, and D.F.Mosher (2010).
Extended binding site on fibronectin for the functional upstream domain of protein F1 of Streptococcus pyogenes.
  J Biol Chem, 285, 41087-41099.  
20739283 M.C.Erat, U.Schwarz-Linek, A.R.Pickford, R.W.Farndale, I.D.Campbell, and I.Vakonakis (2010).
Implications for collagen binding from the crystallographic structure of fibronectin 6FnI1-2FnII7FnI.
  J Biol Chem, 285, 33764-33770.
PDB code: 3mql
20541508 M.Graille, M.Pagano, T.Rose, M.R.Ravaux, and H.van Tilbeurgh (2010).
Zinc induces structural reorganization of gelatin binding domain from human fibronectin and affects collagen binding.
  Structure, 18, 710-718.
PDB code: 3m7p
20541501 R.J.Bingham, and J.R.Potts (2010).
Fibronectin structure: a new piece of the puzzle emerges.
  Structure, 18, 660-661.  
20109226 S.Hoersch, and M.A.Andrade-Navarro (2010).
Periostin shows increased evolutionary plasticity in its alternatively spliced region.
  BMC Evol Biol, 10, 30.  
19401461 A.B.Herr, and R.W.Farndale (2009).
Structural insights into the interactions between platelet receptors and fibrillar collagen.
  J Biol Chem, 284, 19781-19785.  
19366708 I.Vakonakis, D.Staunton, I.R.Ellis, P.Sarkies, A.Flanagan, A.M.Schor, S.L.Schor, and I.D.Campbell (2009).
Motogenic sites in human fibronectin are masked by long range interactions.
  J Biol Chem, 284, 15668-15675.  
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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