1DM0

SHIGA TOXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the holotoxin from Shigella dysenteriae at 2.5 A resolution.

Fraser, M.E.Chernaia, M.M.Kozlov, Y.V.James, M.N.

(1994) Nat Struct Biol 1: 59-64

  • DOI: 10.1038/nsb0194-59
  • Primary Citation of Related Structures:  
    1DM0

  • PubMed Abstract: 
  • Shigella dysenteriae is the pathogen responsible for the severe form of dysentery in humans. It produces Shiga toxin, the prototype of a family of closely related bacterial protein toxins. We have determined the structure of the holotoxin, an AB5 hexamer ...

    Shigella dysenteriae is the pathogen responsible for the severe form of dysentery in humans. It produces Shiga toxin, the prototype of a family of closely related bacterial protein toxins. We have determined the structure of the holotoxin, an AB5 hexamer, by X-ray crystallography. The five B subunits form a pentameric ring, encircling a helix at the carboxy terminus of the A subunit. The A subunit interacts with the B pentamer via this C-terminal helix and a four-stranded mixed beta-sheet. The fold of the rest of the A subunit is similar to that of the A chain of the plant toxin ricin; both are N-glycosidases. However, the active site in the bacterial holotoxin is blocked by a segment of polypeptide chain. These residues of the A subunit would be released as part of the activation mechanism of the toxin.


    Related Citations: 
    • X-ray Crystal Structure of the Shiga Toxin
      Fraser, M.E., Chernaia, M.M., Kozlov, Y.V., James, M.N.
      (1996) Protein Toxin Structure, Parker, M W , Ed --: 173
    • Purification and Crystallization of Shiga Toxin from Shigella dysenteriae
      Kozlov, Y.V., Chernaia, M.M., Fraser, M.E., James, M.N.
      (1993) J Mol Biol 232: 704

    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SHIGA TOXIN A SUBUNIT AL287Shigella dysenteriaeMutation(s): 0 
Gene Names: stxA
EC: 3.2.2.22
Find proteins for Q9FBI2 (Shigella dysenteriae)
Explore Q9FBI2 
Go to UniProtKB:  Q9FBI2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SHIGA TOXIN B SUBUNITBCDEFGHIBCDEFGHIJK
69Shigella dysenteriaeMutation(s): 0 
Gene Names: stxB
Find proteins for Q7BQ98 (Shigella dysenteriae)
Explore Q7BQ98 
Go to UniProtKB:  Q7BQ98
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.05α = 90
b = 147.46β = 90
c = 83.04γ = 90
Software Package:
Software NamePurpose
TNTrefinement
BIOMOLdata reduction
BRUTEmodel building
MLPHAREphasing
DEMONmodel building
X-PLORrefinement
WEISdata scaling
WEISdata reduction
BIOMOLdata scaling
BRUTEphasing
DEMONphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection