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PDBsum entry 1fzd
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protein ligands metals Protein-protein interface(s) links
Blood coagulation PDB id
1fzd

 

 

 

 

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Contents
Protein chain
(+ 2 more) 197 a.a. *
Ligands
NAG-NAG-MAN-MAN-
NAG-MAN ×3
NAG-NDG-MAN-MAN-
NAG-MAN
NAG-NAG ×2
NAG ×4
Metals
_CA ×8
Waters ×496
* Residue conservation analysis
PDB id:
1fzd
Name: Blood coagulation
Title: Structure of recombinant alphaec domain from human fibrinogen-420
Structure: Fibrinogen-420. Chain: a, b, c, d, e, f, g, h. Fragment: alpha-ec domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: blood. Expressed in: pichia pastoris. Expression_system_taxid: 4922
Biol. unit: Octamer (from PQS)
Resolution:
2.10Å     R-factor:   0.199     R-free:   0.255
Authors: G.Spraggon,D.Applegate,S.J.Everse,J.-Z.Zhang,L.Veerapandian,C.Redman, R.F.Doolittle,G.Grieninger
Key ref:
G.Spraggon et al. (1998). Crystal structure of a recombinant alphaEC domain from human fibrinogen-420. Proc Natl Acad Sci U S A, 95, 9099-9104. PubMed id: 9689040 DOI: 10.1073/pnas.95.16.9099
Date:
22-Jun-98     Release date:   19-Aug-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		866 a.a.
197 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.95.16.9099 Proc Natl Acad Sci U S A 95:9099-9104 (1998)
PubMed id: 9689040  
 
 
Crystal structure of a recombinant alphaEC domain from human fibrinogen-420.
G.Spraggon, D.Applegate, S.J.Everse, J.Z.Zhang, L.Veerapandian, C.Redman, R.F.Doolittle, G.Grieninger.
 
  ABSTRACT  
 
The crystal structure of a recombinant alphaEC domain from human fibrinogen-420 has been determined at a resolution of 2.1 A. The protein, which corresponds to the carboxyl domain of the alphaE chain, was expressed in and purified from Pichia pastoris cells. Felicitously, during crystallization an amino-terminal segment was removed, apparently by a contaminating protease, allowing the 201-residue remaining parent body to crystallize. An x-ray structure was determined by molecular replacement. The electron density was clearly defined, partly as a result of averaging made possible by there being eight molecules in the asymmetric unit related by noncrystallographic symmetry (P1 space group). Virtually all of an asparagine-linked sugar cluster is present. Comparison with structures of the beta- and gamma-chain carboxyl domains of human fibrinogen revealed that the binding cleft is essentially neutral and should not bind Gly-Pro-Arg or Gly-His-Arg peptides of the sort bound by those other domains. Nonetheless, the cleft is clearly evident, and the possibility of binding a carbohydrate ligand like sialic acid has been considered.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Crystal of r [E]C domain used for x-ray diffraction study. The crystal measured 0.5 mm on its longest edge. 		Figure 4.
Fig. 4. GRASP (35) depictions of [E]C (Left) and C (Right) domains showing equivalent projections with binding clefts. The ball and stick model is liganded Gly-Pro-Arg-Pro-amide. Note lack of negative charge (red) within the binding site of the [E]C chains.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20427645 C.Schachtrup, J.K.Ryu, M.J.Helmrick, E.Vagena, D.K.Galanakis, J.L.Degen, R.U.Margolis, and K.Akassoglou (2010).
Fibrinogen triggers astrocyte scar formation by promoting the availability of active TGF-beta after vascular damage.
  J Neurosci, 30, 5843-5854.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
15128302 S.Perović-Ottstadt, T.Adell, P.Proksch, M.Wiens, M.Korzhev, V.Gamulin, I.M.Müller, and W.E.Müller (2004).
A (1-->3)-beta-D-glucan recognition protein from the sponge Suberites domuncula. Mediated activation of fibrinogen-like protein and epidermal growth factor gene expression.
  Eur J Biochem, 271, 1924-1937.  
12871291 R.F.Doolittle (2003).
X-ray crystallographic studies on fibrinogen and fibrin.
  J Thromb Haemost, 1, 1559-1565.  
12490209 R.F.Doolittle (2003).
Structural basis of the fibrinogen-fibrin transformation: contributions from X-ray crystallography.
  Blood Rev, 17, 33-41.  
  12617173 S.J.Everse (2002).
New insights into fibrin (ogen) structure and function.
  Vox Sang, 83, 375-382.  
12162736 Z.Yang, G.Spraggon, L.Pandi, S.J.Everse, M.Riley, and R.F.Doolittle (2002).
Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.
  Biochemistry, 41, 10218-10224.
PDB code: 1lwu
10640598 J.L.Cereghino, and J.M.Cregg (2000).
Heterologous protein expression in the methylotrophic yeast Pichia pastoris.
  FEMS Microbiol Rev, 24, 45-66.  
  10880389 S.O.Brennan, J.Wyatt, D.Medicina, F.Callea, and P.M.George (2000).
Fibrinogen brescia: hepatic endoplasmic reticulum storage and hypofibrinogenemia because of a gamma284 Gly-->Arg mutation.
  Am J Pathol, 157, 189-196.  
11123897 S.Yakovlev, S.Litvinovich, D.Loukinov, and L.Medved (2000).
Role of the beta-strand insert in the central domain of the fibrinogen gamma-module.
  Biochemistry, 39, 15721-15729.  
10231539 K.Yokoyama, X.P.Zhang, L.Medved, and Y.Takada (1999).
Specific binding of integrin alpha v beta 3 to the fibrinogen gamma and alpha E chain C-terminal domains.
  Biochemistry, 38, 5872-5877.  
9914253 R.F.Doolittle, G.Spraggon, and S.J.Everse (1998).
Three-dimensional structural studies on fragments of fibrinogen and fibrin.
  Curr Opin Struct Biol, 8, 792-798.  
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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