1DM0

SHIGA TOXIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.Mol.Biol. 1: 59-64


  • 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 hex ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SHIGA TOXIN A SUBUNIT
A, L
287Shigella dysenteriaeMutation(s): 0 
Gene Names: stxA
EC: 3.2.2.22
Find proteins for Q9FBI2 (Shigella dysenteriae)
Go to UniProtKB:  Q9FBI2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SHIGA TOXIN B SUBUNIT
B, C, D, E, F, G, H, I, J, K
69Shigella dysenteriaeMutation(s): 0 
Gene Names: stxB
Find proteins for Q7BQ98 (Shigella dysenteriae)
Go to UniProtKB:  Q7BQ98
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 133.050α = 90.00
b = 147.460β = 90.00
c = 83.040γ = 90.00
Software Package:
Software NamePurpose
BIOMOLdata reduction
DEMONphasing
DEMONmodel building
BRUTEmodel building
MLPHAREphasing
BRUTEphasing
TNTrefinement
WEISdata scaling
WEISdata reduction
BIOMOLdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description