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 

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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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SHIGA-LIKE TOXIN I B SUBUNIT
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
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 
UniProt
Find proteins for P69179 (Enterobacteria phage H19B)
Explore P69179 
Go to UniProtKB:  P69179
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69179
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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],
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]
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G00059MO
GlyCosmos:  G00059MO
GlyGen:  G00059MO
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose
BA [auth b],
BB [auth 1],
DA [auth d],
DB [auth 3],
GB [auth 6],
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
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G67988RO
GlyCosmos:  G67988RO
GlyGen:  G67988RO
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

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Ligand Structure Quality Assessment 


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