PDBsum entry: 1sdd

Blood clotting

PDB id: 1sdd

Contents

Protein chains

268 a.a. *

601 a.a. *

Ligands

NAG ×3

NDG ×2

Metals

_CA

_CU

Waters ×189

* Residue conservation analysis

PDB id:

1sdd

Name:

Blood clotting

Title:

Crystal structure of bovine factor vai

Structure:

Coagulation factor v. Chain: a. Fragment: a1 domain (residues 29-305). Synonym: activated protein c cofactor. Coagulation factor v. Chain: b. Fragment: light chain (a3, c1, c2 domains, residues 1565-22 synonym: activated protein c cofactor

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Other_details: purified from plasma. Other_details: purified from plasma

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.252 R-free: 0.296

Authors:

T.E.Adams,M.F.Hockin,K.G.Mann,S.J.Everse

Key ref:

T.E.Adams et al. (2004). The crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function. Proc Natl Acad Sci U S A, 101, 8918-8923. PubMed id: 15184653 DOI: 10.1073/pnas.0403072101

Date:

13-Feb-04 Release date: 29-Jun-04

Protein chain

Q28107  (FA5_BOVIN) -  Coagulation factor V

Seq: 2211 a.a.

Struc: 268 a.a.

Protein chain

Q28107  (FA5_BOVIN) -  Coagulation factor V

Seq: 2211 a.a.

Struc: 601 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (2 terms)
• Biochemical function: oxidoreductase activity (2 terms)

DOI no: 10.1073/pnas.0403072101

Proc Natl Acad Sci U S A 101:8918-8923 (2004)

PubMed id: 15184653

The crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function.

T.E.Adams, M.F.Hockin, K.G.Mann, S.J.Everse.

ABSTRACT

In vertebrate hemostasis, factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation compared with factor Xa alone. Structurally, little is known about the mechanism by which factor Va alters catalysis within this complex. Here, we report a crystal structure of protein C inactivated factor Va (A1.A3-C1-C2) that depicts a previously uncharacterized domain arrangement. This orientation has implications for binding to membranes essential for function. A high-affinity calcium-binding site and a copper-binding site have both been identified. Surprisingly, neither shows a direct involvement in chain association. This structure represents the largest physiologically relevant fragment of factor Va solved to date and provides a new scaffold for the future generation of models of coagulation cofactors.

Selected figure(s)

Figure 3.
Fig. 3. Stereo images of the metal-binding sites in factor Va[i]. (A) The copper-binding site in the A3 domain (blue) with anomalous density for the copper is shown at 3 . The trigonal planar coordination geometry is shown with dashed lines. Nearby residues from the A1 domain (backbone shaded red) are shown, and the distance to the closest residue is shown in red. (B) The octahedral coordination geometry (dashed lines) of the calcium-binding site in the A1 domain (red).

Figure 4.
Fig. 4. Potential C domain membrane interactions. (A) The membrane-binding spikes of the C1 (Left) and C2 (Right) domains. The domains are displayed in similar orientations with respect to the overall -barrel fold. Residues potentially involved in membrane binding are shown. (B) Packing interactions of the tryptophans from spike C2-1 (2050 and 2051) with a hydrophobic pocket in the A3 domain (white, hydrophobic; blue, polar) from a neighboring molecule.

Figures were selected by an automated process.