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Blood clotting PDB id
1m1j
Jmol
Contents
Protein chains
192 a.a. *
402 a.a. *
390 a.a. *
Ligands
GLY-PRO-ARG-PRO ×2
GLY-HIS-ARG-PRO ×2
NDG ×5
NAG ×3
Metals
_CA ×4
* Residue conservation analysis
PDB id:
1m1j
Name: Blood clotting
Title: Crystal structure of native chicken fibrinogen with two diff bound ligands
Structure: Fibrinogen alpha subunit. Chain: a, d. Fibrinogen beta chain. Chain: b, e. Fibrinogen gamma chain. Chain: c, f. Gly-pro-arg-pro peptide. Chain: g, h. Engineered: yes.
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: blood. Synthetic: yes. Other_details: the peptide is chemically synthesized.. Other_details: the peptide is chemically synthesized.
Biol. unit: 60mer (from PQS)
Resolution:
2.70Å     R-factor:   0.227     R-free:   0.256
Authors: Z.Yang,J.M.Kollman,L.Pandi,R.F.Doolittle
Key ref:
Z.Yang et al. (2001). Crystal structure of native chicken fibrinogen at 2.7 A resolution. Biochemistry, 40, 12515-12523. PubMed id: 11601975 DOI: 10.1021/bi011394p
Date:
19-Jun-02     Release date:   26-Jun-02    
Supersedes: 1jfe
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14448  (FIBA_CHICK) -  Fibrinogen alpha chain
Seq:
Struc: 		 
Seq:
Struc: 		741 a.a.
192 a.a.*
Protein chains
Pfam   ArchSchema ?
Q02020  (FIBB_CHICK) -  Fibrinogen beta chain (Fragment)
Seq:
Struc: 		463 a.a.
402 a.a.
Protein chains
Pfam   ArchSchema ?
O93568  (O93568_CHICK) -  Fibrinogen gamma chain (Precursor)
Seq:
Struc: 		435 a.a.
390 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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  

 

 
DOI no: 10.1021/bi011394p Biochemistry 40:12515-12523 (2001)
PubMed id: 11601975  
 
 
Crystal structure of native chicken fibrinogen at 2.7 A resolution.
Z.Yang, J.M.Kollman, L.Pandi, R.F.Doolittle.
 
  ABSTRACT  
 
The crystal structure of native chicken fibrinogen (320 kDa) complexed with two synthetic peptides has been determined at a resolution of 2.7 A. The structure provides the first atomic-resolution view of the polypeptide chain arrangement in the central domain where the two halves of the molecule are joined, as well as of a putative thrombin-binding site. The amino-terminal segments of the alpha and beta chains, including fibrinopeptides A and B, are not visible in electron density maps, however, and must be highly disordered. The alphaC domain is also very disordered. A residue by residue analysis of the coiled coils with regard to temperature factor shows a strong correlation between mobility and plasmin attack sites. It is concluded that structural flexibility is an inherent feature of fibrinogen that plays a key role in both its conversion to fibrin and its subsequent destruction by plasmin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21475196 P.Macheboeuf, C.Buffalo, C.Y.Fu, A.S.Zinkernagel, J.N.Cole, J.E.Johnson, V.Nizet, and P.Ghosh (2011).
Streptococcal M1 protein constructs a pathological host fibrinogen network.
  Nature, 472, 64-68.
PDB codes: 2xnx 2xny
21106983 T.Riedel, J.Suttnar, E.Brynda, M.Houska, L.Medved, and J.E.Dyr (2011).
Fibrinopeptides A and B release in the process of surface fibrin formation.
  Blood, 117, 1700-1706.  
21054192 T.Thijs, B.P.Nuyttens, H.Deckmyn, and K.Broos (2010).
Platelet physiology and antiplatelet agents.
  Clin Chem Lab Med, 48, S3-13.  
19603492 A.Zagari (2009).
The four cysteines ring motif in proteins.
  Biopolymers, 91, 1048-1055.  
19058845 C.R.Carlisle, C.Coulais, M.Namboothiry, D.L.Carroll, R.R.Hantgan, and M.Guthold (2009).
The mechanical properties of individual, electrospun fibrinogen fibers.
  Biomaterials, 30, 1205-1213.  
19836330 E.H.Lee, J.Hsin, M.Sotomayor, G.Comellas, and K.Schulten (2009).
Discovery through the computational microscope.
  Structure, 17, 1295-1306.  
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.  
19036059 L.Medved, and J.W.Weisel (2009).
Recommendations for nomenclature on fibrinogen and fibrin.
  J Thromb Haemost, 7, 355-359.  
19289066 R.H.Abou-Saleh, S.D.Connell, R.Harrand, R.A.Ajjan, M.W.Mosesson, D.A.Smith, P.J.Grant, and R.A.Ariëns (2009).
Nanoscale probing reveals that reduced stiffness of clots from fibrinogen lacking 42 N-terminal Bbeta-chain residues is due to the formation of abnormal oligomers.
  Biophys J, 96, 2415-2427.  
  19229055 S.O.Brennan, R.L.Davis, R.Lowen, and A.Ruskova (2009).
Deletion of five residues from the coiled coil of fibrinogen (Bbeta Asn167_Glu171del) associated with bleeding and hypodysfibrinogenemia.
  Haematologica, 94, 585-588.  
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.  
18227259 E.J.Walsh, H.Miajlovic, O.V.Gorkun, and T.J.Foster (2008).
Identification of the Staphylococcus aureus MSCRAMM clumping factor B (ClfB) binding site in the alphaC-domain of human fibrinogen.
  Microbiology, 154, 550-558.  
19052234 E.T.O'Brien, M.R.Falvo, D.Millard, B.Eastwood, R.M.Taylor, and R.Superfine (2008).
Ultrathin self-assembled fibrin sheets.
  Proc Natl Acad Sci U S A, 105, 19438-19443.  
18761721 M.R.Falvo, D.Millard, E.T.O'Brien, R.Superfine, and S.T.Lord (2008).
Length of tandem repeats in fibrin's alphaC region correlates with fiber extensibility.
  J Thromb Haemost, 6, 1991-1993.  
18605954 M.Skeppholm, N.H.Wallén, M.Blombäck, and A.Kallner (2008).
Can both EDTA and citrate plasma samples be used in measurements of fibrinogen and C-reactive protein concentrations?
  Clin Chem Lab Med, 46, 1175-1179.  
18549327 P.de Moerloose, and M.Neerman-Arbez (2008).
Treatment of congenital fibrinogen disorders.
  Expert Opin Biol Ther, 8, 979-992.  
18710925 T.A.Springer, J.Zhu, and T.Xiao (2008).
Structural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3.
  J Cell Biol, 182, 791-800.
PDB codes: 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr
18567052 V.Castelletto, G.E.Newby, and I.W.Hamley (2008).
Interactions of KLVFF-PEG peptide conjugate with fibrinogen in neutral aqueous solutions.
  Macromol Biosci, 8, 1182-1189.  
17425334 E.Makogonenko, K.C.Ingham, and L.Medved (2007).
Interaction of the fibronectin COOH-terminal Fib-2 regions with fibrin: further characterization and localization of the Fib-2-binding sites.
  Biochemistry, 46, 5418-5426.  
17681017 E.V.Lugovskoy, P.G.Gritsenko, L.G.Kapustianenko, I.N.Kolesnikova, V.I.Chernishov, and S.V.Komisarenko (2007).
Functional role of Bbeta-chain N-terminal fragment in the fibrin polymerization process.
  FEBS J, 274, 4540-4549.  
17701467 L.C.Serpell, M.Benson, J.J.Liepnieks, and P.E.Fraser (2007).
Structural analyses of fibrinogen amyloid fibrils.
  Amyloid, 14, 199-203.  
17466368 L.C.Xu, and C.A.Siedlecki (2007).
Effects of surface wettability and contact time on protein adhesion to biomaterial surfaces.
  Biomaterials, 28, 3273-3283.  
17952642 M.Guthold, W.Liu, E.A.Sparks, L.M.Jawerth, L.Peng, M.Falvo, R.Superfine, R.R.Hantgan, and S.T.Lord (2007).
A comparison of the mechanical and structural properties of fibrin fibers with other protein fibers.
  Cell Biochem Biophys, 49, 165-181.  
17590019 R.A.Burton, G.Tsurupa, R.R.Hantgan, N.Tjandra, and L.Medved (2007).
NMR solution structure, stability, and interaction of the recombinant bovine fibrinogen alphaC-domain fragment.
  Biochemistry, 46, 8550-8560.
PDB code: 2jor
17630702 R.I.Litvinov, S.Yakovlev, G.Tsurupa, O.V.Gorkun, L.Medved, and J.W.Weisel (2007).
Direct evidence for specific interactions of the fibrinogen alphaC-domains with the central E region and with each other.
  Biochemistry, 46, 9133-9142.  
17414213 S.T.Lord (2007).
Fibrinogen and fibrin: scaffold proteins in hemostasis.
  Curr Opin Hematol, 14, 236-241.  
16879204 B.Blombäck (2006).
Travels with fibrinogen.
  J Thromb Haemost, 4, 1653-1660.  
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
17052980 I.Singh, H.Shankaran, M.E.Beauharnois, Z.Xiao, P.Alexandridis, and S.Neelamegham (2006).
Solution structure of human von Willebrand factor studied using small angle neutron scattering.
  J Biol Chem, 281, 38266-38275.  
16838278 M.Sebbag, N.Moinard, I.Auger, C.Clavel, J.Arnaud, L.Nogueira, J.Roudier, and G.Serre (2006).
Epitopes of human fibrin recognized by the rheumatoid arthritis-specific autoantibodies to citrullinated proteins.
  Eur J Immunol, 36, 2250-2263.  
16230339 P.Panizzi, R.Friedrich, P.Fuentes-Prior, K.Richter, P.E.Bock, and W.Bode (2006).
Fibrinogen substrate recognition by staphylocoagulase.(pro)thrombin complexes.
  J Biol Chem, 281, 1179-1187.  
16475814 R.A.Burton, G.Tsurupa, L.Medved, and N.Tjandra (2006).
Identification of an ordered compact structure within the recombinant bovine fibrinogen alphaC-domain fragment by NMR.
  Biochemistry, 45, 2257-2266.
PDB code: 2baf
16999847 R.Asselta, S.Duga, and M.L.Tenchini (2006).
The molecular basis of quantitative fibrinogen disorders.
  J Thromb Haemost, 4, 2115-2129.  
16288455 R.F.Doolittle, and J.M.Kollman (2006).
Natively unfolded regions of the vertebrate fibrinogen molecule.
  Proteins, 63, 391-397.  
16879216 T.Sugo, H.Endo, M.Matsuda, T.Ohmori, S.Madoiwa, J.Mimuro, and Y.Sakata (2006).
A classification of the fibrin network structures formed from the hereditary dysfibrinogens.
  J Thromb Haemost, 4, 1738-1746.  
15893663 N.Rai, M.Nöllmann, B.Spotorno, G.Tassara, O.Byron, and M.Rocco (2005).
SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics.
  Structure, 13, 723-734.  
14978285 I.Pechik, J.Madrazo, M.W.Mosesson, I.Hernandez, G.L.Gilliland, and L.Medved (2004).
Crystal structure of the complex between thrombin and the central "E" region of fibrin.
  Proc Natl Acad Sci U S A, 101, 2718-2723.
PDB code: 1qvh
15009453 J.W.Weisel (2004).
Cross-linked gamma-chains in fibrin fibrils bridge transversely between strands: no.
  J Thromb Haemost, 2, 394-399.  
15465869 M.Guthold, W.Liu, B.Stephens, S.T.Lord, R.R.Hantgan, D.A.Erie, R.M.Taylor, and R.Superfine (2004).
Visualization and mechanical manipulations of individual fibrin fibers suggest that fiber cross section has fractal dimension 1.3.
  Biophys J, 87, 4226-4236.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
12871284 C.J.Davidson, E.G.Tuddenham, and J.H.McVey (2003).
450 million years of hemostasis.
  J Thromb Haemost, 1, 1487-1494.  
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.  
12241390 F.Ferri, M.Greco, G.Arcòvito, M.De Spirito, and M.Rocco (2002).
Structure of fibrin gels studied by elastic light scattering techniques: dependence of fractal dimension, gel crossover length, fiber diameter, and fiber density on monomer concentration.
  Phys Rev E Stat Nonlin Soft Matter Phys, 66, 011913.  
12009908 G.Tsurupa, L.Tsonev, and L.Medved (2002).
Structural organization of the fibrin(ogen) alpha C-domain.
  Biochemistry, 41, 6449-6459.  
11891217 J.R.Shainoff, G.B.Smejkal, P.M.DiBello, S.S.Sung, L.A.Bush, and E.Di Cera (2002).
Allosteric effects potentiating the release of the second fibrinopeptide A from fibrinogen by thrombin.
  J Biol Chem, 277, 19367-19373.  
11900554 S.Gorlatov, and L.Medved (2002).
Interaction of fibrin(ogen) with the endothelial cell receptor VE-cadherin: mapping of the receptor-binding site in the NH2-terminal portions of the fibrin beta chains.
  Biochemistry, 41, 4107-4116.  
  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
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 codes are shown on the right.