1QNU

Shiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Shiga-like toxins are neutralized by tailored multivalent carbohydrate ligands.

Kitov, P.I.Sadowska, J.M.Mulvey, G.Armstrong, G.D.Ling, H.Pannu, N.S.Read, R.J.Bundle, D.R.

(2000) Nature 403: 669-672

  • DOI: 10.1038/35001095

  • PubMed Abstract: 
  • The diseases caused by Shiga and cholera toxins account for the loss of millions of lives each year. Both belong to the clinically significant subset of bacterial AB5 toxins consisting of an enzymatically active A subunit that gains entry to suscepti ...

    The diseases caused by Shiga and cholera toxins account for the loss of millions of lives each year. Both belong to the clinically significant subset of bacterial AB5 toxins consisting of an enzymatically active A subunit that gains entry to susceptible mammalian cells after oligosaccharide recognition by the B5 homopentamer. Therapies might target the obligatory oligosaccharide-toxin recognition event, but the low intrinsic affinity of carbohydrate-protein interactions hampers the development of low-molecular-weight inhibitors. The toxins circumvent low affinity by binding simultaneously to five or more cell-surface carbohydrates. Here we demonstrate the use of the crystal structure of the B5 subunit of Escherichia coli O157:H7 Shiga-like toxin I (SLT-I) in complex with an analogue of its carbohydrate receptor to design an oligovalent, water-soluble carbohydrate ligand (named STARFISH), with subnanomolar inhibitory activity. The in vitro inhibitory activity is 1-10-million-fold higher than that of univalent ligands and is by far the highest molar activity of any inhibitor yet reported for Shiga-like toxins I and II. Crystallography of the STARFISH/Shiga-like toxin I complex explains this activity. Two trisaccharide receptors at the tips of each of five spacer arms simultaneously engage all five B subunits of two toxin molecules.


    Related Citations: 
    • Structure of the Shiga-Like Toxin I B-Pentamer Complexed with an Analogue of its Receptor Bg3
      Ling, H.,Boodhoo, A.,Hazes, B.,Cummings, M.D.,Armstrong, G.D.,Brunton, J.L.,Read, R.J.
      (1998) Biochemistry 37: 1777


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shiga toxin 1 variant B subunit
A, B, C, D, E
69Shigella phage 75/02 StxMutation(s): 0 
Find proteins for V5URS0 (Shigella phage 75/02 Stx)
Go to UniProtKB:  V5URS0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMB
Query on EMB

Download SDF File 
Download CCD File 
A, B, C, D, E
METHYL-CARBAMIC ACID ETHYL ESTER
C4 H9 N O2
SURZCVYFPAXNGN-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B, C, D, E
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B, C, D, E
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
MEC
Query on MEC

Download SDF File 
Download CCD File 
A, B, C, D, E
ETHYL-CARBAMIC ACID METHYL ESTER
C4 H9 N O2
AEARPZNULDFPNQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.470α = 90.00
b = 71.610β = 109.02
c = 56.360γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-05-30
    Type: Data collection, Structure summary
  • Version 1.4: 2018-06-13
    Type: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation