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

 

 

 

 

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Contents
Protein chains
81 a.a. *
309 a.a. *
303 a.a. *
Ligands
NAG ×4
Metals
_CA ×6
* Residue conservation analysis
PDB id:
1fze
Name: Blood coagulation
Title: Crystal structure of fragment double-d from human fibrin
Structure: Fibrinogen. Chain: a, d. Fragment: fragment d. Fibrinogen. Chain: b, e. Fragment: fragment d. Fibrinogen. Chain: c, f. Fragment: fragment d
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: blood. Tissue: blood. Tissue: blood
Biol. unit: Trimer (from PQS)
Resolution:
3.00Å     R-factor:   0.251     R-free:   0.318
Authors: S.J.Everse,G.Spraggon,L.Veerapandian,R.F.Doolittle
Key ref:
S.J.Everse et al. (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. PubMed id: 10074346 DOI: 10.1021/bi982626w
Date:
23-Dec-98     Release date:   08-Jun-99    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		866 a.a.
81 a.a.
Protein chains
Pfam   ArchSchema ?
P02675  (FIBB_HUMAN) -  Fibrinogen beta chain from Homo sapiens
Seq:
Struc: 		491 a.a.
309 a.a.
Protein chains
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain from Homo sapiens
Seq:
Struc: 		453 a.a.
303 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi982626w Biochemistry 38:2941-2946 (1999)
PubMed id: 10074346  
 
 
Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide.
S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle.
 
  ABSTRACT  
 
The structure of fragment double-D from human fibrin has been solved in the presence and absence of the peptide ligands that simulate the two knobs exposed by the removal of fibrinopeptides A and B, respectively. All told, six crystal structures have been determined, three of which are reported here for the first time: namely, fragments D and double-D with the peptide GHRPam alone and double-D in the absence of any peptide ligand. Comparison of the structures has revealed a series of conformational changes that are brought about by the various knob-hole interactions. Of greatest interest is a moveable "flap" of two negatively charged amino acids (Glubeta397 and Aspbeta398) whose side chains are pinned back to the coiled coil with a calcium atom bridge until GHRPam occupies the beta-chain pocket. Additionally, in the absence of the peptide ligand GPRPam, GHRPam binds to the gamma-chain pocket, a new calcium-binding site being formed concomitantly.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19650644 S.R.Bowley, N.Okumura, and S.T.Lord (2009).
Impaired protofibril formation in fibrinogen gamma N308K is due to altered D:D and "A:a" interactions.
  Biochemistry, 48, 8656-8663.
PDB code: 3hus
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
18818200 I.Parastatidis, L.Thomson, A.Burke, I.Chernysh, C.Nagaswami, J.Visser, S.Stamer, D.C.Liebler, G.Koliakos, H.F.Heijnen, G.A.Fitzgerald, J.W.Weisel, and H.Ischiropoulos (2008).
Fibrinogen beta-chain tyrosine nitration is a prothrombotic risk factor.
  J Biol Chem, 283, 33846-33853.  
17090548 A.A.Amelot, M.Tagzirt, G.Ducouret, R.L.Kuen, and B.F.Le Bonniec (2007).
Platelet factor 4 (CXCL4) seals blood clots by altering the structure of fibrin.
  J Biol Chem, 282, 710-720.  
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.  
17922803 J.W.Weisel (2007).
Which knobs fit into which holes in fibrin polymerization?
  J Thromb Haemost, 5, 2340-2343.  
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.  
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
16575257 R.C.Marchi, Z.Carvajal, C.Boyer-Neumann, E.Anglés-Cano, and J.W.Weisel (2006).
Functional characterization of fibrinogen Bicêtre II: a gamma 308 Asn-->Lys mutation located near the fibrin D:D interaction sites.
  Blood Coagul Fibrinolysis, 17, 193-201.  
15869595 M.Hirota-Kawadobora, S.Kani, F.Terasawa, N.Fujihara, K.Yamauchi, M.Tozuka, and N.Okumura (2005).
Functional analysis of recombinant Bbeta15C and Bbeta15A fibrinogens demonstrates that Bbeta15G residue plays important roles in FPB release and in lateral aggregation of protofibrils.
  J Thromb Haemost, 3, 983-990.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
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.  
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
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.  
10933802 J.L.Mullin, O.V.Gorkun, and S.T.Lord (2000).
Decreased lateral aggregation of a variant recombinant fibrinogen provides insight into the polymerization mechanism.
  Biochemistry, 39, 9843-9849.  
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.  
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.  
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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