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Blood clotting PDB id
1ei3
Jmol
Contents
Protein chains
159 a.a.* *
395 a.a.* *
397 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1ei3
Name: Blood clotting
Title: Crystal structure of native chicken fibrinogen
Structure: Fibrinogen. Chain: a, d. Fragment: alpha chain. Fibrinogen. Chain: b, e. Fragment: beta chain. Fibrinogen. Chain: c, f. Fragment: gamma chain
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organism_taxid: 9031
Resolution:
5.50Å     R-factor:   not given    
Authors: Z.Yang,I.Mochalkin,L.Veerapandian,M.Riley,R.F.Doolittle
Key ref:
Z.Yang et al. (2000). Crystal structure of native chicken fibrinogen at 5.5-A resolution. Proc Natl Acad Sci U S A, 97, 3907-3912. PubMed id: 10737772 DOI: 10.1073/pnas.080065697
Date:
23-Feb-00     Release date:   10-May-00    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14448  (FIBA_CHICK) -  Fibrinogen alpha chain
Seq:
Struc: 		 
Seq:
Struc: 		741 a.a.
159 a.a.
Protein chains
Pfam   ArchSchema ?
Q02020  (FIBB_CHICK) -  Fibrinogen beta chain (Fragment)
Seq:
Struc: 		463 a.a.
395 a.a.
Protein chains
Pfam   ArchSchema ?
O93568  (O93568_CHICK) -  Fibrinogen gamma chain (Precursor)
Seq:
Struc: 		435 a.a.
397 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   7 terms 
  Biological process     signal transduction   5 terms 
  Biochemical function     receptor binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.080065697 Proc Natl Acad Sci U S A 97:3907-3912 (2000)
PubMed id: 10737772  
 
 
Crystal structure of native chicken fibrinogen at 5.5-A resolution.
Z.Yang, I.Mochalkin, L.Veerapandian, M.Riley, R.F.Doolittle.
 
  ABSTRACT  
 
The crystal structure of native chicken fibrinogen has been determined at a resolution of 5.5 A. The full-length molecule is 460 A in length and sigmoidally shaped. The structure includes the full sweep of the coiled coils that connect the central and terminal domains; the chain paths of the central domain confirm a predicted scheme of planar disulfide rings in apposition with each other. Electron density maps have revealed the outlines of disordered alphaC domains nestled within the confines of the sinuous coiled coils. The amino-terminal segments of the alpha- and beta-chains, including the fibrinopeptides A and B, are also disordered.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Schematic depiction of -, -, and -chains of chicken (Ch) and human (Hu) fibrinogens showing missing repeat region (10 × 13 resolution, stippled) from chicken -chains. Dark shading, homologous central domains and coiled-coil regions. Light shading, homologous C and C domains. Asterisks (*) denote locations of disulfide ring cysteines; scale shows chain lengths in residues. (Inset) SDS/5% polyacrylamide gels of human (H) and chicken (C) fibrinogens. Lanes 1 and 2, unreduced; lanes 3 and 4, reduced. Note that chicken -chains are only slightly larger than -chains. 		Figure 3.
Fig. 3. Section of an electron density map calculated at 8 Å showing native chicken fibrinogen mainframe backbone density (blue) and disordered regions of C domains (gray). The figure was prepared with the program RIBBON (35).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19603492 A.Zagari (2009).
The four cysteines ring motif in proteins.
  Biopolymers, 91, 1048-1055.  
19928926 G.Tsurupa, R.R.Hantgan, R.A.Burton, I.Pechik, N.Tjandra, and L.Medved (2009).
Structure, stability, and interaction of the fibrin(ogen) alphaC-domains.
  Biochemistry, 48, 12191-12201.  
19630789 J.K.Ryu, D.Davalos, and K.Akassoglou (2009).
Fibrinogen signal transduction in the nervous system.
  J Thromb Haemost, 7, 151-154.  
19420351 T.A.Morris, J.J.Marsh, P.G.Chiles, M.M.Magaña, N.C.Liang, X.Soler, D.J.Desantis, D.Ngo, and V.L.Woods (2009).
High prevalence of dysfibrinogenemia among patients with chronic thromboembolic pulmonary hypertension.
  Blood, 114, 1929-1936.  
16533041 I.Pechik, S.Yakovlev, M.W.Mosesson, G.L.Gilliland, and L.Medved (2006).
Structural basis for sequential cleavage of fibrinopeptides upon fibrin assembly.
  Biochemistry, 45, 3588-3597.
PDB code: 2a45
16999847 R.Asselta, S.Duga, and M.L.Tenchini (2006).
The molecular basis of quantitative fibrinogen disorders.
  J Thromb Haemost, 4, 2115-2129.  
15665082 T.Vorup-Jensen, C.V.Carman, M.Shimaoka, P.Schuck, J.Svitel, and T.A.Springer (2005).
Exposure of acidic residues as a danger signal for recognition of fibrinogen and other macromolecules by integrin alphaXbeta2.
  Proc Natl Acad Sci U S A, 102, 1614-1619.  
15238080 B.Rubin, and G.Sønderstrup (2004).
Citrullination of self-proteins and autoimmunity.
  Scand J Immunol, 60, 112-120.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
14519075 C.A.Staton, N.J.Brown, and C.E.Lewis (2003).
The role of fibrinogen and related fragments in tumour angiogenesis and metastasis.
  Expert Opin Biol Ther, 3, 1105-1120.  
  12490209 R.F.Doolittle (2003).
Structural basis of the fibrinogen-fibrin transformation: contributions from X-ray crystallography.
  Blood Rev, 17, 33-41.  
12009908 G.Tsurupa, L.Tsonev, and L.Medved (2002).
Structural organization of the fibrin(ogen) alpha C-domain.
  Biochemistry, 41, 6449-6459.  
11877740 H.S.Park, C.Kim, and Y.K.Kang (2002).
Preferred conformations of RGDX tetrapeptides to inhibit the binding of fibrinogen to platelets.
  Biopolymers, 63, 298-313.  
11928820 K.Akassoglou, and S.Strickland (2002).
Nervous system pathology: the fibrin perspective.
  Biol Chem, 383, 37-45.  
12231361 M.A.Arnaout, S.L.Goodman, and J.P.Xiong (2002).
Coming to grips with integrin binding to ligands.
  Curr Opin Cell Biol, 14, 641-651.  
12115462 M.Conti, G.Donati, G.Cianciolo, S.Stefoni, and B.Samorì (2002).
Force spectroscopy study of the adhesion of plasma proteins to the surface of a dialysis membrane: role of the nanoscale surface hydrophobicity and topography.
  J Biomed Mater Res, 61, 370-379.  
12089331 S.Akhter, A.Vignini, Z.Wen, A.English, P.G.Wang, and B.Mutus (2002).
Evidence for S-nitrosothiol-dependent changes in fibrinogen that do not involve transnitrosation or thiolation.
  Proc Natl Acad Sci U S A, 99, 9172-9177.  
  12617173 S.J.Everse (2002).
New insights into fibrin (ogen) structure and function.
  Vox Sang, 83, 375-382.  
11308648 F.Ferri, M.Greco, G.Arcovito, F.A.Bassi, M.De Spirito, E.Paganini, and M.Rocco (2001).
Growth kinetics and structure of fibrin gels.
  Phys Rev E Stat Nonlin Soft Matter Phys, 63, 031401.  
11593005 J.Madrazo, J.H.Brown, S.Litvinovich, R.Dominguez, S.Yakovlev, L.Medved, and C.Cohen (2001).
Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution.
  Proc Natl Acad Sci U S A, 98, 11967-11972.
PDB codes: 1jy2 1jy3
11400130 T.H.Barker, G.M.Fuller, M.M.Klinger, D.S.Feldman, and J.S.Hagood (2001).
Modification of fibrinogen with poly(ethylene glycol) and its effects on fibrin clot characteristics.
  J Biomed Mater Res, 56, 529-535.  
11121023 Z.Yang, I.Mochalkin, and R.F.Doolittle (2000).
A model of fibrin formation based on crystal structures of fibrinogen and fibrin fragments complexed with synthetic peptides.
  Proc Natl Acad Sci U S A, 97, 14156-14161.  
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.