1BOS

SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3.

Ling, H.Boodhoo, A.Hazes, B.Cummings, M.D.Armstrong, G.D.Brunton, J.L.Read, R.J.

(1998) Biochemistry 37: 1777-1788

  • DOI: 10.1021/bi971806n
  • Primary Citation of Related Structures:  
    1BOS

  • PubMed Abstract: 
  • Shiga-like toxin I (SLT-I) is a virulence factor of Escherichia coli strains that cause disease in humans. Like other members of the Shiga toxin family, it consists of an enzymatic (A) subunit and five copies of a binding subunit (the B-pentamer). The B-pentamer binds to a specific glycolipid, globotriaosylceramide (Gb3), on the surface of target cells and thereby plays a crucial role in the entry of the toxin ...

    Shiga-like toxin I (SLT-I) is a virulence factor of Escherichia coli strains that cause disease in humans. Like other members of the Shiga toxin family, it consists of an enzymatic (A) subunit and five copies of a binding subunit (the B-pentamer). The B-pentamer binds to a specific glycolipid, globotriaosylceramide (Gb3), on the surface of target cells and thereby plays a crucial role in the entry of the toxin. Here we present the crystal structure at 2.8 A resolution of the SLT-I B-pentamer complexed with an analogue of the Gb3 trisaccharide. The structure reveals a surprising density of binding sites, with three trisaccharide molecules bound to each B-subunit monomer of 69 residues. All 15 trisaccharides bind to one side of the B-pentamer, providing further evidence that this side faces the cell membrane. The structural model is consistent with data from site-directed mutagenesis and binding of carbohydrate analogues, and allows the rational design of therapeutic Gb3 analogues that block the attachment of toxin to cells.


    Related Citations: 
    • Crystal Structure of the Cell-Binding B Oligomer of Verotoxin-1 from E. Coli
      Stein, P.E., Boodhoo, A., Tyrrell, G.J., Brunton, J.L., Read, R.J.
      (1992) Nature 355: 748

    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-LIKE TOXIN I B SUBUNIT
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
69Phage h30Enterobacteria phage H-19B
This entity is chimeric
Mutation(s): 0 
Find proteins for P69179 (Enterobacteria phage H19B)
Explore P69179 
Go to UniProtKB:  P69179
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
AA [auth a], AB [auth 0], CA [auth c], CB [auth 2], EA [auth e], EB [auth 4], FA [auth f], FB [auth 5]
AA [auth a], AB [auth 0], CA [auth c], CB [auth 2], EA [auth e], EB [auth 4], FA [auth f], FB [auth 5], GA [auth g], HA [auth h], HB [auth 7], IA [auth i], IB [auth 8], JA [auth j], JB [auth 9], KA [auth k], KB [auth AA], LB [auth BA], MA [auth m], MB [auth CA], OA [auth o], OB [auth EA], PA [auth p], PB [auth FA], RA [auth r], SA [auth s], TA [auth t], U, VA [auth v], W, X, XA [auth x], ZA [auth z]
3 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose
BA [auth b], BB [auth 1], DA [auth d], DB [auth 3], GB [auth 6], LA [auth l], NA [auth n], NB [auth DA]
BA [auth b], BB [auth 1], DA [auth d], DB [auth 3], GB [auth 6], LA [auth l], NA [auth n], NB [auth DA], QA [auth q], QB [auth GA], UA [auth u], V, WA [auth w], Y, YA [auth y], Z
2 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.5α = 90
b = 97.7β = 90
c = 164.2γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Advisory, Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary