4K1P

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 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 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 B ...

    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.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of the NheA component of the Nhe toxin from Bacillus cereus.
      Phung, D., Ganash, M., Sedelnikova, S.E., Lindback, T., Granum, P.E., Artymiuk, P.J.
      (2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1073

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NheAABCDEFGH360Bacillus cereusMutation(s): 0 
Gene Names: nheAnheABC (operon)B1995_19070BACERE00183_04930CNQ78_07165
Find proteins for Q3Y6N6 (Bacillus cereus)
Explore Q3Y6N6 
Go to UniProtKB:  Q3Y6N6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, D, E, G
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • 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 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references