4H56

Crystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.284 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Architecture and Functional Analysis of NetB, a Pore-forming Toxin from Clostridium perfringens.

Savva, C.G.Fernandes da Costa, S.P.Bokori-Brown, M.Naylor, C.E.Cole, A.R.Moss, D.S.Titball, R.W.Basak, A.K.

(2013) J.Biol.Chem. 288: 3512-3522

  • DOI: 10.1074/jbc.M112.430223

  • PubMed Abstract: 
  • NetB is a pore-forming toxin produced by Clostridium perfringens and has been reported to play a major role in the pathogenesis of avian necrotic enteritis, a disease that has emerged due to the removal of antibiotics in animal feedstuffs. Here we pr ...

    NetB is a pore-forming toxin produced by Clostridium perfringens and has been reported to play a major role in the pathogenesis of avian necrotic enteritis, a disease that has emerged due to the removal of antibiotics in animal feedstuffs. Here we present the crystal structure of the pore form of NetB solved to 3.9 Å. The heptameric assembly shares structural homology to the staphylococcal α-hemolysin. However, the rim domain, a region that is thought to interact with the target cell membrane, shows sequence and structural divergence leading to the alteration of a phosphocholine binding pocket found in the staphylococcal toxins. Consistent with the structure we show that NetB does not bind phosphocholine efficiently but instead interacts directly with cholesterol leading to enhanced oligomerization and pore formation. Finally we have identified conserved and non-conserved amino acid positions within the rim loops that significantly affect binding and toxicity of NetB. These findings present new insights into the mode of action of these pore-forming toxins, enabling the design of more effective control measures against necrotic enteritis and providing potential new tools to the field of bionanotechnology.


    Organizational Affiliation

    Department of Biological Sciences, School of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London, WC1E 7HX, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Necrotic enteritis toxin B
A, B, C, D, E, F, G, H, I, J, K, L, M, N
296Clostridium perfringensMutation(s): 0 
Gene Names: netB
Find proteins for A8ULG6 (Clostridium perfringens)
Go to UniProtKB:  A8ULG6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.284 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 313.230α = 90.00
b = 168.040β = 109.42
c = 160.460γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
SCALAdata scaling
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2013-03-06
    Type: Database references