1CZS

CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: COMPLEX WITH PHENYLMERCURY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the membrane-binding C2 domain of human coagulation factor V.

Macedo-Ribeiro, S.Bode, W.Huber, R.Quinn-Allen, M.A.Kim, S.W.Ortel, T.L.Bourenkov, G.P.Bartunik, H.D.Stubbs, M.T.Kane, W.H.Fuentes-Prior, P.

(1999) Nature 402: 434-439

  • DOI: 10.1038/46594
  • Primary Citation of Related Structures:  
    1CZV, 1CZT, 1CZS

  • PubMed Abstract: 
  • Rapid and controlled clot formation is achieved through sequential activation of circulating serine proteinase precursors on phosphatidylserine-rich procoagulant membranes of activated platelets and endothelial cells. The homologous complexes Xase and prothrombinase, each consisting of an active proteinase and a non-enzymatic cofactor, perform critical steps within this coagulation cascade ...

    Rapid and controlled clot formation is achieved through sequential activation of circulating serine proteinase precursors on phosphatidylserine-rich procoagulant membranes of activated platelets and endothelial cells. The homologous complexes Xase and prothrombinase, each consisting of an active proteinase and a non-enzymatic cofactor, perform critical steps within this coagulation cascade. The activated cofactors VIIIa and Va, highly specific for their cognate proteinases, are each derived from precursors with the same A1-A2-B-A3-C1-C2 architecture. Membrane binding is mediated by the C2 domains of both cofactors. Here we report two crystal structures of the C2 domain of human factor Va. The conserved beta-barrel framework provides a scaffold for three protruding loops, one of which adopts markedly different conformations in the two crystal forms. We propose a mechanism of calcium-independent, stereospecific binding of factors Va and VIIIa to phospholipid membranes, on the basis of (1) immersion of hydrophobic residues at the apices of these loops in the apolar membrane core; (2) specific interactions with phosphatidylserine head groups in the groove enclosed by these loops; and (3) favourable electrostatic contacts of basic side chains with negatively charged membrane phosphate groups.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Martinsried, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (COAGULATION FACTOR V)A160Homo sapiensMutation(s): 0 
Gene Names: F5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P12259 (Homo sapiens)
Explore P12259 
Go to UniProtKB:  P12259
PHAROS:  P12259
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHG
Query on PHG

Download Ideal Coordinates CCD File 
B [auth A]PHENYLMERCURY
C6 H5 Hg
DCNLOVYDMCVNRZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.43α = 90
b = 51.83β = 90
c = 68.15γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance