2G7C

Clostridium difficile Toxin A Fragment Bound to aGal(1,3)bGal(1,4)bGlcNAc

• PDB DOI: https://doi.org/10.2210/pdb2G7C/pdb

• Classification: TOXIN
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-02-28 Released: 2006-04-18 
• Deposition Author(s): Greco, A., Ho, J.G.S., Lin, S.J., Palcic, M.M., Rupnik, M., Ng, K.K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Carbohydrate recognition by Clostridium difficile toxin A.

Greco, A., Ho, J.G., Lin, S.J., Palcic, M.M., Rupnik, M., Ng, K.K.

(2006) Nat Struct Mol Biol 13: 460-461

• PubMed: 16622409 
• DOI: https://doi.org/10.1038/nsmb1084
• Primary Citation of Related Structures:  
  2G7C


• PubMed Abstract: 
  

  Clostridium difficile TcdA is a large toxin that binds carbohydrates on intestinal epithelial cells. A 2-A resolution cocrystal structure reveals two molecules of alpha-Gal-(1,3)-beta-Gal-(1,4)-beta-GlcNAcO(CH(2))(8)CO(2)CH(3) binding in an extended conformation to TcdA. Residues forming key contacts with the trisaccharides are conserved in all seven putative binding sites in TcdA, suggesting a mode of multivalent binding that may be exploited for the rational design of novel therapeutics.

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Organizational Affiliation: 

Alberta Ingenuity Centre for Carbohydrate Science, University of Calgary, Calgary, Canada T2N 1N4.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.02 kDa 
• Atom Count: 4,588 
• Modelled Residue Count: 499 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin A	A, B	255	Clostridioides difficile	Mutation(s): 14  Gene Names: toxA, tcdA EC: 3.4.22
UniProt
Find proteins for P16154 (Clostridioides difficile) Explore P16154  Go to UniProtKB:  P16154

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	3		N/A
Glycosylation Resources
GlyTouCan:  G03499BP GlyCosmos:  G03499BP GlyGen:  G03499BP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.682	α = 90
b = 132.825	β = 100.29
c = 65.917	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Greco, A., Ho, J.G.S., Lin, S.J., Palcic, M.M., Rupnik, M., Ng, K.K.S.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2022-12-21
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-20
  Changes: Data collection, Refinement description