3W57 | pdb_00003w57

Structure of a C2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.182 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3W57

This is version 1.3 of the entry. See complete history

Literature

Defining the interaction of perforin with calcium and the phospholipid membrane.

Traore, D.A.Brennan, A.J.Law, R.H.Dogovski, C.Perugini, M.A.Lukoyanova, N.Leung, E.W.Norton, R.S.Lopez, J.A.Browne, K.A.Yagita, H.Lloyd, G.J.Ciccone, A.Verschoor, S.Trapani, J.A.Whisstock, J.C.Voskoboinik, I.

(2013) Biochem J 456: 323-335

  • DOI: https://doi.org/10.1042/BJ20130999
  • Primary Citation Related Structures: 
    3W56, 3W57

  • PubMed Abstract: 

    Following its secretion from cytotoxic lymphocytes into the immune synapse, perforin binds to target cell membranes through its Ca(2+)-dependent C2 domain. Membrane-bound perforin then forms pores that allow passage of pro-apoptopic granzymes into the target cell. In the present study, structural and biochemical studies reveal that Ca(2+) binding triggers a conformational change in the C2 domain that permits four key hydrophobic residues to interact with the plasma membrane. However, in contrast with previous suggestions, these movements and membrane binding do not trigger irreversible conformational changes in the pore-forming MACPF (membrane attack complex/perforin-like) domain, indicating that subsequent monomer-monomer interactions at the membrane surface are required for perforin pore formation.


  • Organizational Affiliation
    • ††Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, U.K.

Macromolecule Content 

  • Total Structure Weight: 30.82 kDa 
  • Atom Count: 2,214 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 262 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C2 domain protein
A, B
131Scophthalmus maximusMutation(s): 0 
Gene Names: C2P1
Membrane Entity: Yes 
UniProt
Find proteins for E2FYL5 (Scophthalmus maximus)
Explore E2FYL5 
Go to UniProtKB:  E2FYL5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE2FYL5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.182 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.803α = 90
b = 52.751β = 107.15
c = 49.055γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary