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, by X-ray crystallography ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SHIGA TOXIN A SUBUNITA,
B [auth L]		287Shigella dysenteriaeMutation(s): 0 
Gene Names: stxA
EC: 3.2.2.22
UniProt
Find proteins for Q9FBI2 (Shigella dysenteriae)
Explore Q9FBI2 
Go to UniProtKB:  Q9FBI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FBI2
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SHIGA TOXIN B SUBUNIT69Shigella dysenteriaeMutation(s): 0 
Gene Names: stxB
UniProt
Find proteins for Q7BQ98 (Shigella dysenteriae)
Explore Q7BQ98 
Go to UniProtKB:  Q7BQ98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7BQ98
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

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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