Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.99 kDa 
• Atom Count: 2338 
• Residue Count: 266 
• Unique protein chains: 2

4NBX

Crystal Structure of Clostridium difficile Toxin A fragment TcdA-A1 Bound to A20.1 VHH

• DOI: 10.2210/pdb4NBX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Clostridioides difficile, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-23 Released: 2013-12-11 
• Deposition Author(s): Murase, T., Eugenio, L., Schorr, M., Hussack, G., Tanha, J., Kitova, E.N., Klassen, J.S., Ng, K.K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.229 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile.

Murase, T., Eugenio, L., Schorr, M., Hussack, G., Tanha, J., Kitova, E.N., Klassen, J.S., Ng, K.K.

(2014) J Biol Chem 289: 2331-2343

• PubMed: 24311789 
• DOI: 10.1074/jbc.M113.505917
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents.

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Organizational Affiliation: 

From the Department of Biological Sciences and Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 1N4, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TcdA	A	143	Clostridioides difficile	Mutation(s): 0  Gene Names: tcdA
Find proteins for I6YE93 (Clostridioides difficile) Go to UniProtKB:  I6YE93

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
A20.1 VHH	B	154	Lama glama	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.229 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.97	α = 90
b = 96.97	β = 90
c = 61.12	γ = 120

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-23 
• Released Date: 2013-12-11 
Deposition Author(s): Murase, T., Eugenio, L., Schorr, M., Hussack, G., Tanha, J., Kitova, E.N., Klassen, J.S., Ng, K.K.S.

Revision History 

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2014-01-01
  Changes: Database references
• Version 1.2: 2014-02-12
  Changes: Database references