2BOS | pdb_00002bos

A MUTANT SHIGA-LIKE TOXIN IIE BOUND TO ITS RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.194 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history

Literature

A mutant Shiga-like toxin IIe bound to its receptor Gb(3): structure of a group II Shiga-like toxin with altered binding specificity.

Ling, H.Pannu, N.S.Boodhoo, A.Armstrong, G.D.Clark, C.G.Brunton, J.L.Read, R.J.

(2000) Structure 8: 253-264

  • DOI: https://doi.org/10.1016/s0969-2126(00)00103-9
  • Primary Citation Related Structures: 
    1QOH, 2BOS

  • PubMed Abstract: 

    Shiga-like toxins (SLTs) are produced by the pathogenic strains of Escherichia coli that cause hemorrhagic colitis and hemolytic uremic syndrome. These diseases in humans are generally associated with group II family members (SLT-II and SLT-IIc), whereas SLT-IIe (pig edema toxin) is central to edema disease of swine. The pentameric B-subunit component of the majority of family members binds to the cell-surface glycolipid globotriaosyl ceramide (Gb(3)), but globotetraosyl ceramide (Gb(4)) is the preferred receptor for SLT-IIe. A double-mutant of the SLT-IIe B subunit that reverses two sequence differences from SLT-II (GT3; Gln65-->Glu, Lys67-->Gln, SLT-I numbering) has been shown to bind more strongly to Gb(3) than to Gb(4). To understand the molecular basis of receptor binding and specificity, we have determined the structure of the GT3 mutant B pentamer, both in complex with a Gb(3) analogue (2.0 A resolution; R = 0.155, R(free) = 0.194) and in its native form (2.35 A resolution; R = 0.187, R(free) = 0.232). These are the first structures of a member of the medically important group II Shiga-like toxins to be reported. The structures confirm the previous observation of multiple binding sites on each SLT monomer, although binding site 3 is not occupied in the GT3 structure. Analysis of the binding properties of mutants suggests that site 3 is a secondary Gb(4)-binding site. The two mutated residues are located appropriately to interact with the extra betaGalNAc residue on Gb(4). Differences in the binding sites provide a molecular basis for understanding the tissue specificities and pathogenic mechanisms of members of the SLT family.


  • Organizational Affiliation
    • Department of Biochemistry, University of Alberta, Edmonton, T6G 2H7, Canada.

Macromolecule Content 

  • Total Structure Weight: 41.33 kDa 
  • Atom Count: 3,078 
  • Modeled Residue Count: 340 
  • Deposited Residue Count: 340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
A, B, C, D, E
68Escherichia coliMutation(s): 2 
UniProt
Find proteins for Q47644 (Escherichia coli)
Explore Q47644 
Go to UniProtKB:  Q47644
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47644
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
F, G, H, J, K
3N/A
Glycosylation Resources
GlyTouCan: G79094AA
GlyCosmos: G79094AA
GlyGen: G79094AA
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose
I, L
2N/A
Glycosylation Resources
GlyTouCan: G67988RO
GlyCosmos: G67988RO
GlyGen: G67988RO

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.194 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.077α = 90
b = 78.618β = 90
c = 78.468γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
AMoREphasing
BRUTEmodel building
X-PLORrefinement
BRUTEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-20
    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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-16
    Changes: Structure summary