4K1P | pdb_00004k1p

Structure of the NheA component of the Nhe toxin from Bacillus cereus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.262 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the NheA Component of the Nhe Toxin from Bacillus cereus: Implications for Function.

Ganash, M.Phung, D.Sedelnikova, S.E.Lindback, T.Granum, P.E.Artymiuk, P.J.

(2013) PLoS One 8: e74748-e74748

  • DOI: https://doi.org/10.1371/journal.pone.0074748
  • Primary Citation of Related Structures:  
    4K1P

  • PubMed Abstract: 

    The structure of NheA, a component of the Bacillus cereus Nhe tripartite toxin, has been solved at 2.05 Å resolution using selenomethionine multiple-wavelength anomalous dispersion (MAD). The structure shows it to have a fold that is similar to the Bacillus cereus Hbl-B and E. coli ClyA toxins, and it is therefore a member of the ClyA superfamily of α-helical pore forming toxins (α-PFTs), although its head domain is significantly enlarged compared with those of ClyA or Hbl-B. The hydrophobic β-hairpin structure that is a characteristic of these toxins is replaced by an amphipathic β-hairpin connected to the main structure via a β-latch that is reminiscent of a similar structure in the β-PFT Staphylococcus aureus α-hemolysin. Taken together these results suggest that, although it is a member of an archetypal α-PFT family of toxins, NheA may be capable of forming a β rather than an α pore.


  • Organizational Affiliation

    The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NheA
A, B, C, D, E
A, B, C, D, E, F, G, H
360Bacillus cereusMutation(s): 0 
Gene Names: nheAnheABC (operon)
UniProt
Find proteins for Q3Y6N6 (Bacillus cereus)
Explore Q3Y6N6 
Go to UniProtKB:  Q3Y6N6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3Y6N6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.262 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 309.008α = 90
b = 58.242β = 110.61
c = 172.999γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
xia2data reduction
SCALEPACKdata scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations