4H56

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.285 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1074/jbc.M112.430223
  • Primary Citation of Related Structures:  
    4H56

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Necrotic enteritis toxin B
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
296Clostridium perfringensMutation(s): 0 
Gene Names: netB
Membrane Entity: Yes 
UniProt
Find proteins for A8ULG6 (Clostridium perfringens)
Explore A8ULG6 
Go to UniProtKB:  A8ULG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8ULG6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 313.23α = 90
b = 168.04β = 109.42
c = 160.46γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2013-03-06
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description