Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystal structure of a calcium-phospholipid binding domain from cytosolic phospholipase A2.

Perisic, O.Fong, S.Lynch, D.E.Bycroft, M.Williams, R.L.

(1998) J Biol Chem 273: 1596-1604

  • DOI: https://doi.org/10.1074/jbc.273.3.1596
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cytosolic phospholipase A2 (cPLA2) is a calcium-sensitive 85-kDa enzyme that hydrolyzes arachidonic acid-containing membrane phospholipids to initiate the biosynthesis of eicosanoids and platelet-activating factor, potent inflammatory mediators. The calcium-dependent activation of the enzyme is mediated by an N-terminal C2 domain, which is responsible for calcium-dependent translocation of the enzyme to membranes and that enables the intact enzyme to hydrolyze membrane-resident substrates. The 2.4-A x-ray crystal structure of this C2 domain was solved by multiple isomorphous replacement and reveals a beta-sandwich with the same topology as the C2 domain from phosphoinositide-specific phospholipase C delta 1. Two clusters of exposed hydrophobic residues surround two adjacent calcium binding sites. This region, along with an adjoining strip of basic residues, appear to constitute the membrane binding motif. The structure provides a striking insight into the relative importance of hydrophobic and electrostatic components of membrane binding for cPLA2. Although hydrophobic interactions predominate for cPLA2, for other C2 domains such as in "conventional" protein kinase C and synaptotagmins, electrostatic forces prevail.

  • Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Medical Research Council Centre, Cambridge, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2126Homo sapiensMutation(s): 2 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P47712 (Homo sapiens)
Explore P47712 
Go to UniProtKB:  P47712
PHAROS:  P47712
GTEx:  ENSG00000116711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47712
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
CA BindingDB:  1RLW ΔH: -2.60e+1 (kJ/mol) from 1 assay(s)
ΔG: -3.32e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.41α = 90
b = 79.41β = 90
c = 70.67γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-02-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection