Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.83 kDa 
• Atom Count: 4966 
• Modelled Residue Count: 588 
• Deposited Residue Count: 630 
• Unique protein chains: 1

3DWA

Crystal structure of the B-subunit of the AB5 toxin from E. coli

• PDB DOI: 10.2210/pdb3DWA/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-22 Released: 2008-11-04 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.236 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

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

• PubMed: 18971931 
• DOI: 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.

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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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilase cytotoxin, subunit B	A, B, C, D, E	126	Escherichia coli	Mutation(s): 0  Gene Names: subB, LH0182
UniProt
Find proteins for Q3ZTX8 (Escherichia coli) Explore Q3ZTX8  Go to UniProtKB:  Q3ZTX8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.236 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.63	α = 90
b = 97.63	β = 90
c = 165.36	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-22 
• Released Date: 2008-11-04 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance