spacer
spacer

PDBsum entry 1rf1

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Blood clotting PDB id
1rf1
Jmol
Contents
Protein chains
64 a.a. *
299 a.a. *
298 a.a. *
56 a.a. *
Ligands
GLY-HIS-ARG-PRO ×4
NAG-NAG-FUC ×2
Metals
_CA ×4
Waters ×248
* Residue conservation analysis
PDB id:
1rf1
Name: Blood clotting
Title: Crystal structure of fragment d of gammae132a fibrinogen wit peptide ligand gly-his-arg-pro-amide
Structure: Fibrinogen alpha/alpha-e chain. Chain: a, d. Fragment: fibrinogen alpha/alpha-e chain. Engineered: yes. Fibrinogen beta chain. Chain: b, e. Fragment: fibrinogen bbeta chain. Engineered: yes. Fibrinogen gamma chain.
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: Pentamer (from PQS)
Resolution:
2.53Å     R-factor:   0.234     R-free:   0.281
Authors: M.S.Kostelansky,O.V.Gorkun,S.T.Lord
Key ref:
M.S.Kostelansky et al. (2004). Calcium-binding site beta 2, adjacent to the "b" polymerization site, modulates lateral aggregation of protofibrils during fibrin polymerization. Biochemistry, 43, 2475-2483. PubMed id: 14992585 DOI: 10.1021/bi0359978
Date:
07-Nov-03     Release date:   16-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
Seq:
Struc:
 
Seq:
Struc:
866 a.a.
64 a.a.
Protein chains
Pfam   ArchSchema ?
P02675  (FIBB_HUMAN) -  Fibrinogen beta chain
Seq:
Struc:
491 a.a.
299 a.a.
Protein chains
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain
Seq:
Struc:
453 a.a.
298 a.a.*
Protein chain
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
Seq:
Struc:
 
Seq:
Struc:
866 a.a.
56 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/bi0359978 Biochemistry 43:2475-2483 (2004)
PubMed id: 14992585  
 
 
Calcium-binding site beta 2, adjacent to the "b" polymerization site, modulates lateral aggregation of protofibrils during fibrin polymerization.
M.S.Kostelansky, K.C.Lounes, L.F.Ping, S.K.Dickerson, O.V.Gorkun, S.T.Lord.
 
  ABSTRACT  
 
Structural analysis of recombinant fibrinogen fragment D revealed that the calcium-binding site (beta2-site) composed of residues BbetaAsp261, BbetaAsp398, BbetaGly263, and gammaGlu132 is modulated by the "B:b" interaction. To determine the beta2-site's role in polymerization, we engineered variant fibrinogen gammaE132A in which calcium binding to the beta2-site was disrupted by replacing glutamic acid at gamma132 with alanine. We compared polymerization of gammaE132A to normal fibrinogen as a function of calcium concentration. Polymerization of gammaE132A at concentrations of calcium <or=1 mM exhibited an uncharacteristic 2-3-fold increase in lateral aggregation and fiber thickness compared to normal fibrinogen, while polymerization of variant and normal were indistinguishable at 10 mM calcium. These results suggest that the beta2-site controls the extent of lateral aggregation. That is, when the calcium anchor (beta2-site) is eliminated before "B:b" interactions occur then lateral aggregation is enhanced. We solved structures of fragment D of gammaE132A fibrinogen (rfD-gammaE132A) with and without Gly-His-Arg-Pro-amide (GHRPam) and found no change to the global structure. X-ray diffraction data showed GHRPam binding in the "a" and "b" polymerization sites and that calcium could still bind to the beta2-site of gammaE132A fibrinogen at 70 mM calcium. We found that the gamma2 calcium-binding site (in loop gamma294-301) did not have calcium bound in the structure of fragment D of gammaE132A fibrinogen with GHRPam bound (rfD-gammaE132A+GH). Analysis of structures rfD-gammaE132A+GH and rfD-BbetaD398A+GH indicated that differences in calcium occupation of the gamma2-site resulted from minor conformational changes provoked by crystal packing and GHRPam binding to the "a" site did not directly modulate calcium binding to this site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20228273 N.J.Mutch, R.Engel, S.Uitte de Willige, H.Philippou, and R.A.Ariëns (2010).
Polyphosphate modifies the fibrin network and down-regulates fibrinolysis by attenuating binding of tPA and plasminogen to fibrin.
  Blood, 115, 3980-3988.  
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
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.  
17922803 J.W.Weisel (2007).
Which knobs fit into which holes in fibrin polymerization?
  J Thromb Haemost, 5, 2340-2343.  
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.  
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.