1CZV | pdb_00001czv

CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: DIMERIC CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.257 (Depositor) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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: https://doi.org/10.1038/46594
  • Primary Citation Related Structures: 
    1CZS, 1CZT, 1CZV

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 37.22 kDa 
  • Atom Count: 2,704 
  • Modeled Residue Count: 318 
  • Deposited Residue Count: 320 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (COAGULATION FACTOR V)
A, B
160Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P12259 (Homo sapiens)
Explore P12259 
Go to UniProtKB:  P12259
PHAROS:  P12259
GTEx:  ENSG00000198734 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12259
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.257 (Depositor) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.52α = 90
b = 70.54β = 90
c = 60.58γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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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
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary