PDBsum entry: 1rf1

Blood clotting

PDB id: 1rf1

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

Protein chain

P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain

Seq: 866 a.a.

Struc: 64 a.a.

Protein chains

P02675  (FIBB_HUMAN) -  Fibrinogen beta chain

Seq: 491 a.a.

Struc: 299 a.a.

Protein chains

P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain

Seq: 453 a.a.

Struc: 298 a.a.*

Protein chain

P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain

Seq: 866 a.a.

Struc: 56 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular space (2 terms)
• 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.