Crystal structure of the A-subunit of the AB5 toxin from E. coli with Neu5Gc-2,3Gal-1,3GlcNAc

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin

Byres, E.Paton, A.W.Paton, J.C.Lofling, J.C.Smith, D.F.Wilce, M.C.J.Talbot, U.M.Chong, D.C.Yu, H.Huang, S.Chen, X.Varki, N.M.Varki, A.Rossjohn, J.Beddoe, T.

(2008) Nature 456: 648-652

  • DOI: https://doi.org/10.1038/nature07428
  • Primary Citation of Related Structures:  
    3DWA, 3DWP, 3DWQ

  • PubMed Abstract: 

    AB(5) toxins comprise an A subunit that corrupts essential eukaryotic cell functions, and pentameric B subunits that direct target-cell uptake after binding surface glycans. Subtilase cytotoxin (SubAB) is an AB(5) toxin secreted by Shiga toxigenic Escherichia coli (STEC), which causes serious gastrointestinal disease in humans. SubAB causes haemolytic uraemic syndrome-like pathology in mice through SubA-mediated cleavage of BiP/GRP78, an essential endoplasmic reticulum chaperone. Here we show that SubB has a strong preference for glycans terminating in the sialic acid N-glycolylneuraminic acid (Neu5Gc), a monosaccharide not synthesized in humans. Structures of SubB-Neu5Gc complexes revealed the basis for this specificity, and mutagenesis of key SubB residues abrogated in vitro glycan recognition, cell binding and cytotoxicity. SubAB specificity for Neu5Gc was confirmed using mouse tissues with a human-like deficiency of Neu5Gc and human cell lines fed with Neu5Gc. Despite lack of Neu5Gc biosynthesis in humans, assimilation of dietary Neu5Gc creates high-affinity receptors on human gut epithelia and kidney vasculature. This, and the lack of Neu5Gc-containing body fluid competitors in humans, confers susceptibility to the gastrointestinal and systemic toxicities of SubAB. Ironically, foods rich in Neu5Gc are the most common source of STEC contamination. Thus a bacterial toxin's receptor is generated by metabolic incorporation of an exogenous factor derived from food.

  • Organizational Affiliation

    Protein Crystallography Unit and ARC Centre of Excellence for Structural and Functional Microbial Genomics, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subtilase cytotoxin, subunit B
A, B, C, D, E
126Escherichia coliMutation(s): 0 
Gene Names: subB
Find proteins for Q3ZTX8 (Escherichia coli)
Explore Q3ZTX8 
Go to UniProtKB:  Q3ZTX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3ZTX8
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
F, G, H, I
Glycosylation Resources
GlyTouCan:  G23068ZB
GlyCosmos:  G23068ZB
GlyGen:  G23068ZB
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1PE

Download Ideal Coordinates CCD File 
L [auth A],
M [auth B],
R [auth D],
S [auth D],
V [auth E]
C10 H22 O6
Query on POL

Download Ideal Coordinates CCD File 
J [auth A],
N [auth C],
P [auth D],
T [auth E]
C3 H8 O
Query on AZI

Download Ideal Coordinates CCD File 
K [auth A],
O [auth C],
Q [auth D],
U [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.253α = 90
b = 97.253β = 90
c = 163.52γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary