4M1U

The crystal structure of Stx2 and a disaccharide ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of shiga toxin type 2 with bound disaccharide guides the design of a heterobifunctional toxin inhibitor.

Jacobson, J.M.Yin, J.Kitov, P.I.Mulvey, G.Griener, T.P.James, M.N.Armstrong, G.Bundle, D.R.

(2014) J.Biol.Chem. 289: 885-894

  • DOI: 10.1074/jbc.M113.518886

  • PubMed Abstract: 
  • Shiga toxin type 2 (Stx2a) is clinically most closely associated with enterohemorrhagic E. coli O157:H7-mediated hemorrhagic colitis that sometimes progresses to hemolytic-uremic syndrome. The ability to express the toxin has been acquired by other E ...

    Shiga toxin type 2 (Stx2a) is clinically most closely associated with enterohemorrhagic E. coli O157:H7-mediated hemorrhagic colitis that sometimes progresses to hemolytic-uremic syndrome. The ability to express the toxin has been acquired by other Escherichia coli strains, and outbreaks of food poisoning have caused significant mortality rates as, for example, in the 2011 outbreak in northern Germany. Stx2a, an AB5 toxin, gains entry into human cells via the glycosphingolipid receptor Gb3. We have determined the first crystal structure of a disaccharide analog of Gb3 bound to the B5 pentamer of Stx2a holotoxin. In this Gb3 analog,-GalNAc replaces the terminal-Gal residue. This co-crystal structure confirms previous inferences that two of the primary binding sites identified in theB5 pentamer of Stx1 are also functional in Stx2a. This knowledge provides a rationale for the synthesis and evaluation of heterobifunctional antagonists for E. coli toxins that target Stx2a. Incorporation of GalNAc Gb3 trisaccharide in a heterobifunctional ligand with an attached pyruvate acetal, a ligand for human amyloid P component, and conjugation to poly[acrylamide-co-(3-azidopropylmethacrylamide)] produced a polymer that neutralized Stx2a in a mouse model of Shigatoxemia.


    Organizational Affiliation

    From the Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shiga toxin 2 A-subunit
A
297Escherichia coli O157:H7Gene Names: stx2 A-subunit (stx 2 A-subunit, stx2A)
Find proteins for Q7DI68 (Escherichia coli O157:H7)
Go to UniProtKB:  Q7DI68
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Shiga toxin 2 B subunit
B, C, D, E, F
70Escherichia coliGene Names: stxII (stx2B, stx2dB, stx2vB, stxB2, vtx2B)
Find proteins for Q7DJJ2 (Escherichia coli)
Go to UniProtKB:  Q7DJJ2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PS
Query on 1PS

Download SDF File 
Download CCD File 
B, C, D
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
1-(3-SULFOPROPYL) PYRIDINIUM, PPS
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
 Ligand Interaction
MBG
Query on MBG

Download SDF File 
Download CCD File 
F
METHYL-BETA-GALACTOSE
C7 H14 O6
HOVAGTYPODGVJG-VOQCIKJUSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
F
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 146.250α = 90.00
b = 146.250β = 90.00
c = 60.310γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
MxDCdata collection
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-12-04
    Type: Database references
  • Version 1.2: 2014-02-19
    Type: Database references