Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.20 kDa 
• Atom Count: 1155 
• Residue Count: 125 
• Unique protein chains: 1

2F6E

Clostridium difficile Toxin A C-terminal fragment 1 (TcdA-f1)

• DOI: 10.2210/pdb2F6E/pdb

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


• Deposited: 2005-11-29 Released: 2005-12-20 
• Deposition Author(s): Ng, K.K., Ho, J.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Crystal structure of receptor-binding C-terminal repeats from Clostridium difficile toxin A

Ho, J.G., Greco, A., Rupnik, M., Ng, K.K.

(2005) Proc Natl Acad Sci U S A 102: 18373-18378

• PubMed: 16344467 
• DOI: 10.1073/pnas.0506391102
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Clostridium difficile is a major nosocomial pathogen that produces two large protein toxins [toxin A (TcdA) and toxin B (TcdB)] capable of disrupting intestinal epithelial cells. Both belong to the family of large clostridial cytotoxins, which are characterized by the presence of a repetitive C-terminal repetitive domain (CRD). In TcdA, the CRD is composed of 39 repeats that are responsible for binding to cell surface carbohydrates. To understand the molecular structural basis of cell binding by the toxins from C. difficile, we have determined a 1.85-A resolution crystal structure of a 127-aa fragment from the C terminus of the toxin A CRD. This structure reveals a beta-solenoid fold containing five repeats, with each repeat consisting of a beta-hairpin followed by a loop of 7-10 residues in short repeats (SRs) or 18 residues in long repeats (LRs). Adjacent pairs of beta-hairpins are related to each other by either 90 degree or 120 degree screw-axis rotational relationships, depending on the nature of the amino acids at key positions in adjacent beta-hairpins. Models of the complete CRDs of toxins A and B suggest that each CRD contains straight stretches of beta-solenoid composed of three to five SRs that are punctuated by kinks introduced by the presence of a single LR. These structural features provide a framework for understanding how large clostridial cytotoxins bind to cell surfaces and suggest approaches for developing novel treatments for C. difficile-associated diseases by blocking the binding of toxins to cell surfaces.

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Organizational Affiliation: 

Alberta Ingenuity Centre for Carbohydrate Sciences, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Toxin A	A	127	Clostridioides difficile	Mutation(s): 0  Gene Names: toxA, tcdA EC: 3.4.22
Find proteins for P16154 (Clostridioides difficile) Go to UniProtKB:  P16154

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.05	α = 90
b = 42.05	β = 90
c = 132.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-29 
• Released Date: 2005-12-20 
Deposition Author(s): Ng, K.K., Ho, J.G.

Revision History 

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance