PDBsum entry 1fzc

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protein ligands metals Protein-protein interface(s) links
Blood coagulation PDB id
Protein chains
74 a.a. *
308 a.a. *
301 a.a. *
NAG ×4
_CA ×4
Waters ×431
* Residue conservation analysis
PDB id:
Name: Blood coagulation
Title: Crystal structure of fragment double-d from human fibrin wit different bound ligands
Structure: Fibrin. Chain: a, d. Fragment: double-d. Fibrin. Chain: b, e. Fragment: double-d. Fibrin. Chain: c, f. Fragment: double-d.
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: blood. Tissue: blood. Tissue: blood
Biol. unit: Pentamer (from PQS)
2.30Å     R-factor:   0.220     R-free:   0.290
Authors: S.J.Everse,G.Spraggon,L.Veerapandian,M.Riley,R.F.Doolittle
Key ref:
S.J.Everse et al. (1998). Crystal structure of fragment double-D from human fibrin with two different bound ligands. Biochemistry, 37, 8637-8642. PubMed id: 9628725 DOI: 10.1021/bi9804129
19-May-98     Release date:   14-Oct-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
866 a.a.
74 a.a.
Protein chains
Pfam   ArchSchema ?
P02675  (FIBB_HUMAN) -  Fibrinogen beta chain
491 a.a.
308 a.a.
Protein chains
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain
453 a.a.
301 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     fibrinogen complex   1 term 
  Biological process     signal transduction   3 terms 
  Biochemical function     receptor binding     2 terms  


DOI no: 10.1021/bi9804129 Biochemistry 37:8637-8642 (1998)
PubMed id: 9628725  
Crystal structure of fragment double-D from human fibrin with two different bound ligands.
S.J.Everse, G.Spraggon, L.Veerapandian, M.Riley, R.F.Doolittle.
Factor XIII-cross-linked fragment D (double-D) from human fibrin was crystallized in the presence of two different peptide ligands and the X-ray structure determined at 2.3 A. The peptide Gly-Pro-Arg-Pro-amide, which is an analogue of the knob exposed by the thrombin-catalyzed removal of fibrinopeptide A, was found to reside in the gamma-chain holes, and the peptide Gly-His-Arg-Pro-amide, which corresponds to the beta-chain knob, was found in the homologous beta-chain holes. The structure shows for the first time that the beta-chain knob does indeed bind to a homologous hole on the beta-chain. The gamma- and beta-chain holes are structurally very similar, and it is remarkable they are able to distinguish between these two peptides that differ by a single amino acid. Additionally, we have found that the beta-chain domain, like its gamma-chain counterpart, binds calcium.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21435714 A.S.Soon, C.S.Lee, and T.H.Barker (2011).
Modulation of fibrin matrix properties via knob:hole affinity interactions using peptide-PEG conjugates.
  Biomaterials, 32, 4406-4414.  
  20606742 A.Cortelazzo, R.Guerranti, L.Bini, N.Hope-Onyekwere, C.Muzzi, R.Leoncini, and R.Pagani (2010).
Effects of snake venom proteases on human fibrinogen chains.
  Blood Transfus, 8, s120-s125.  
19914710 A.S.Soon, S.E.Stabenfeldt, W.E.Brown, and T.H.Barker (2010).
Engineering fibrin matrices: the engagement of polymerization pockets through fibrin knob technology for the delivery and retention of therapeutic proteins.
  Biomaterials, 31, 1944-1954.  
19075185 S.R.Bowley, and S.T.Lord (2009).
Fibrinogen variant BbetaD432A has normal polymerization but does not bind knob "B".
  Blood, 113, 4425-4430.
PDB code: 3e1i
19746505 T.Bornschlögl, J.C.Gebhardt, and M.Rief (2009).
Designing the folding mechanics of coiled coils.
  Chemphyschem, 10, 2800-2804.  
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.  
17892530 C.B.Geer, A.Tripathy, M.H.Schoenfisch, S.T.Lord, and O.V.Gorkun (2007).
Role of 'B-b' knob-hole interactions in fibrin binding to adsorbed fibrinogen.
  J Thromb Haemost, 5, 2344-2351.  
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.  
17883696 N.Dib, F.Quelin, C.Ternisien, M.Hanss, S.Michalak, P.De Mazancourt, M.C.Rousselet, and P.Calès (2007).
Fibrinogen angers with a new deletion (gamma GVYYQ 346-350) causes hypofibrinogenemia with hepatic storage.
  J Thromb Haemost, 5, 1999-2005.  
16940416 R.I.Litvinov, O.V.Gorkun, D.K.Galanakis, S.Yakovlev, L.Medved, H.Shuman, and J.W.Weisel (2007).
Polymerization of fibrin: Direct observation and quantification of individual B:b knob-hole interactions.
  Blood, 109, 130-138.  
17414213 S.T.Lord (2007).
Fibrinogen and fibrin: scaffold proteins in hemostasis.
  Curr Opin Hematol, 14, 236-241.  
16689770 L.Betts, B.K.Merenbloom, and S.T.Lord (2006).
The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE.
  J Thromb Haemost, 4, 1139-1141.
PDB code: 2ffd
16999847 R.Asselta, S.Duga, and M.L.Tenchini (2006).
The molecular basis of quantitative fibrinogen disorders.
  J Thromb Haemost, 4, 2115-2129.  
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.  
16102057 M.W.Mosesson (2005).
Fibrinogen and fibrin structure and functions.
  J Thromb Haemost, 3, 1894-1904.  
15723073 P.Petzelbauer, P.A.Zacharowski, Y.Miyazaki, P.Friedl, G.Wickenhauser, F.J.Castellino, M.Gröger, K.Wolff, and K.Zacharowski (2005).
The fibrin-derived peptide Bbeta15-42 protects the myocardium against ischemia-reperfusion injury.
  Nat Med, 11, 298-304.  
15653148 R.Gorodetsky, N.Peylan-Ramu, A.Reshef, E.Gaberman, L.Levdansky, and G.Marx (2005).
Interactions of carboplatin with fibrin(ogen), implications for local slow release chemotherapy.
  J Control Release, 102, 235-245.  
15998829 R.I.Litvinov, O.V.Gorkun, S.F.Owen, H.Shuman, and J.W.Weisel (2005).
Polymerization of fibrin: specificity, strength, and stability of knob-hole interactions studied at the single-molecule level.
  Blood, 106, 2944-2951.  
16207719 V.B.Louvain-Quintard, E.P.Bianchini, C.Calmel-Tareau, M.Tagzirt, and B.F.Le Bonniec (2005).
Thrombin-activable factor X re-establishes an intrinsic amplification in tenase-deficient plasmas.
  J Biol Chem, 280, 41352-41359.  
15304042 M.Hirota-Kawadobora, F.Terasawa, T.Suzuki, M.Tozuka, K.Sano, and N.Okumura (2004).
Comparison of thrombin-catalyzed fibrin polymerization and factor XIIIa-catalyzed cross-linking of fibrin among three recombinant variant fibrinogens, gamma 275C, gamma 275H, and gamma 275A.
  J Thromb Haemost, 2, 1359-1367.  
15389122 R.C.Marchi, M.H.Meyer, Bosch, C.L.Arocha-Piñango, and J.W.Weisel (2004).
A novel mutation (deletion of Aalpha-Asn 80) in an abnormal fibrinogen: fibrinogen Caracas VI. Consequences of disruption of the coiled coil for the polymerization of fibrin: peculiar clot structure and diminished stiffness of the clot.
  Blood Coagul Fibrinolysis, 15, 559-567.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
15009465 S.Ishikawa, M.Hirota-Kawadobora, M.Tozuka, K.Ishii, F.Terasawa, and N.Okumura (2004).
Recombinant fibrinogen, gamma275Arg-->Cys, exhibits formation of disulfide bond with cysteine and severely impaired D:D interactions.
  J Thromb Haemost, 2, 468-475.  
14567695 A.Profumo, M.Turci, G.Damonte, F.Ferri, D.Magatti, B.Cardinali, C.Cuniberti, and M.Rocco (2003).
Kinetics of fibrinopeptide release by thrombin as a function of CaCl2 concentration: different susceptibility of FPA and FPB and evidence for a fibrinogen isoform-specific effect at physiological Ca2+ concentration.
  Biochemistry, 42, 12335-12348.  
12871494 M.W.Mosesson (2003).
Fibrinogen gamma chain functions.
  J Thromb Haemost, 1, 231-238.  
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.  
12009908 G.Tsurupa, L.Tsonev, and L.Medved (2002).
Structural organization of the fibrin(ogen) alpha C-domain.
  Biochemistry, 41, 6449-6459.  
  12617173 S.J.Everse (2002).
New insights into fibrin (ogen) structure and function.
  Vox Sang, 83, 375-382.  
11901150 T.Rose, and E.Di Cera (2002).
Three-dimensional modeling of thrombin-fibrinogen interaction.
  J Biol Chem, 277, 18875-18880.  
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
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
10618375 J.H.Brown, N.Volkmann, G.Jun, A.H.Henschen-Edman, and C.Cohen (2000).
The crystal structure of modified bovine fibrinogen.
  Proc Natl Acad Sci U S A, 97, 85-90.
PDB code: 1deq
10866981 S.Bernocco, F.Ferri, A.Profumo, C.Cuniberti, and M.Rocco (2000).
Polymerization of rod-like macromolecular monomers studied by stopped-flow, multiangle light scattering: set-up, data processing, and application to fibrin formation.
  Biophys J, 79, 561-583.  
11123898 S.Yakovlev, E.Makogonenko, N.Kurochkina, W.Nieuwenhuizen, K.Ingham, and L.Medved (2000).
Conversion of fibrinogen to fibrin: mechanism of exposure of tPA- and plasminogen-binding sites.
  Biochemistry, 39, 15730-15741.  
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.  
10737772 Z.Yang, I.Mochalkin, L.Veerapandian, M.Riley, and R.F.Doolittle (2000).
Crystal structure of native chicken fibrinogen at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 97, 3907-3912.
PDB code: 1ei3
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.  
10074346 S.J.Everse, G.Spraggon, L.Veerapandian, and R.F.Doolittle (1999).
Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide.
  Biochemistry, 38, 2941-2946.
PDB codes: 1fze 1fzf 1fzg
9689040 G.Spraggon, D.Applegate, S.J.Everse, J.Z.Zhang, L.Veerapandian, C.Redman, R.F.Doolittle, and G.Grieninger (1998).
Crystal structure of a recombinant alphaEC domain from human fibrinogen-420.
  Proc Natl Acad Sci U S A, 95, 9099-9104.
PDB code: 1fzd
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.