PDBsum entry 1re4

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protein ligands metals Protein-protein interface(s) links
Blood clotting PDB id
Protein chains
65 a.a. *
306 a.a. *
298 a.a. *
60 a.a. *
NAG ×2
_CA ×6
Waters ×164
* Residue conservation analysis
PDB id:
Name: Blood clotting
Title: Crystal structure of fragment d of bbetad398a fibrinogen
Structure: Fibrinogen alpha/alpha-e chain. Chain: a, d. Fragment: fragment d of fibrinogen alpha chain. Engineered: yes. Fibrinogen beta chain. Chain: b, e. Fragment: fragment d of bbetad398a fibrinogen beta chain. Engineered: yes. Mutation: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: fga. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: cho. Expression_system_organ: ovary. Gene: fgb.
Biol. unit: Trimer (from PQS)
2.70Å     R-factor:   0.220     R-free:   0.271
Authors: M.S.Kostelansky,L.Betts,O.V.Gorkun,S.T.Lord
Key ref:
M.S.Kostelansky et al. (2004). B beta Glu397 and B beta Asp398 but not B beta Asp432 are required for "B:b" interactions. Biochemistry, 43, 2465-2474. PubMed id: 14992584 DOI: 10.1021/bi035996f
06-Nov-03     Release date:   25-May-04    
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Protein chain
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
866 a.a.
65 a.a.
Protein chains
Pfam   ArchSchema ?
P02675  (FIBB_HUMAN) -  Fibrinogen beta chain
491 a.a.
306 a.a.*
Protein chains
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain
453 a.a.
298 a.a.
Protein chain
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
866 a.a.
60 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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/bi035996f Biochemistry 43:2465-2474 (2004)
PubMed id: 14992584  
B beta Glu397 and B beta Asp398 but not B beta Asp432 are required for "B:b" interactions.
M.S.Kostelansky, B.Bolliger-Stucki, L.Betts, O.V.Gorkun, S.T.Lord.
We synthesized three fibrinogen variants, BbetaE397A, BbetaD398A, and BbetaD432A, with substitutions at positions identified in crystallographic studies as critical for binding the "B" peptide, Gly-His-Arg-Pro-amide (GHRPam), to the "b" polymerization site. We examined thrombin- and batroxobin-catalyzed polymerization by turbidity measurements and found that BbetaE397A and BbetaD398A were impaired while BbetaD432A was normal. Changes in polymerization as a function of calcium were similar for variant and normal fibrinogens. We determined crystal structures of fragment D from the variant BbetaD398A in the absence and presence of GHRPam. In the absence of peptide, the structure showed that the alanine substitution altered only specific local interactions, as alignment of the variant structure with the analogous normal structure resulted in an RMSD of 0.53 A over all atoms. The structure also showed reduced occupancy of the beta2 calcium-binding site that includes the side chain carbonyl of BbetaD398, suggesting that calcium was not bound at this site in our polymerization studies. In the presence of peptide, the structure showed that GHRPam was not bound in the "b" site and the conformational changes associated with peptide binding to normal fragment D did not occur. This structure also showed GHRPam bound in the "a" polymerization site, although in two different conformations. Calcium binding was associated with only one of these conformations, suggesting that calcium binding to the gamma2-site and an alternative peptide conformation were induced by crystal packing. We conclude that BbetaE397 and BbetaD398 are essential for the "B:b" interaction, while BbetaD432 is not.

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
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.  
17922804 N.Okumura, F.Terasawa, A.Haneishi, N.Fujihara, M.Hirota-Kawadobora, K.Yamauchi, H.Ota, and S.T.Lord (2007).
B:b interactions are essential for polymerization of variant fibrinogens with impaired holes 'a'.
  J Thromb Haemost, 5, 2352-2359.  
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.  
16689768 M.H.Horellou, C.Chevreaud, V.Mathieux, J.Conard, and Mazancourt (2006).
Fibrinogen Paris IX: a case of symptomatic hypofibrinogenemia with Bbeta Y236C and Bbeta IVS7-1G-->C mutations.
  J Thromb Haemost, 4, 1134-1136.  
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.