Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - ABCDE Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer -A2B2C 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 123971.21 
• Atom Count: 6855 
• Residue Count: 1135 
• Unique protein chains: 3

5UMI

Clostridium difficile TcdA-CROPs bound to PA50 Fab

• DOI: 10.2210/pdb5UMI/pdb

• Classification: TOXIN/IMMUNE SYSTEM
• Organism(s): Clostridioides difficile
• Expression System: Cricetulus griseus, Bacillus megaterium


• Deposited: 2017-01-27 Released: 2017-07-19 
• Deposition Author(s): Kroh, H.K., Chandrasekaran, R., Rosenthal, K., Woods, R., Jin, X., Ohi, M.D., Nyborg, A.C., Rainey, G.J., Warrener, P., Spiller, B.W., Lacy, D.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 0.290 
• R-Value Work: 0.270 

Literature

Use of a neutralizing antibody helps identify structural features critical for binding of Clostridium difficile toxin TcdA to the host cell surface.

Kroh, H.K., Chandrasekaran, R., Rosenthal, K., Woods, R., Jin, X., Ohi, M.D., Nyborg, A.C., Rainey, G.J., Warrener, P., Spiller, B.W., Lacy, D.B.

(2017) J. Biol. Chem. 292: 14401-14412

• PubMed: 28705932 
• DOI: 10.1074/jbc.M117.781112


• PubMed Abstract: 
  

Clostridium difficile is a clinically significant pathogen that causes mild-to-severe (and often recurrent) colon infections. Disease symptoms stem from the activities of two large, multidomain toxins known as TcdA and TcdB. The toxins can bind, enter, and perturb host cell function through a multistep mechanism of receptor binding, endocytosis, pore formation, autoproteolysis, and glucosyltransferase-mediated modification of host substrates. Monoclonal antibodies that neutralize toxin activity provide a survival benefit in preclinical animal models and prevent recurrent infections in human clinical trials. However, the molecular mechanisms involved in these neutralizing activities are unclear. To this end, we performed structural studies on a neutralizing monoclonal antibody, PA50, a humanized mAb with both potent and broad-spectrum neutralizing activity, in complex with TcdA. Electron microscopy imaging and multiangle light-scattering analysis revealed that PA50 binds multiple sites on the TcdA C-terminal combined repetitive oligopeptides (CROPs) domain. A crystal structure of two PA50 Fabs bound to a segment of the TcdA CROPs helped define a conserved epitope that is distinct from previously identified carbohydrate-binding sites. Binding of TcdA to the host cell surface was directly blocked by either PA50 mAb or Fab and suggested that receptor blockade is the mechanism by which PA50 neutralizes TcdA. These findings highlight the importance of the CROPs C terminus in cell-surface binding and a role for neutralizing antibodies in defining structural features critical to a pathogen's mechanism of action. We conclude that PA50 protects host cells by blocking the binding of TcdA to cell surfaces.

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Organizational Affiliation: 

From the Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2363.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Toxin A	C	271	Clostridioides difficile	Mutation(s): 0  Gene Names: toxA (tcdA) EC: 3.4.22.-
Find proteins for P16154 (Clostridioides difficile) Go to UniProtKB:  P16154

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PA50 Fab Light chain	L, B	211	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PA50 Fab Heavy chain	H, A	221	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 0.290 
• R-Value Work: 0.270 
• Space Group: P 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 93.685	α = 90.00
b = 77.330	β = 90.91
c = 97.781	γ = 90.00

Software Package:

Software Name	Purpose
xia2	data reduction
xia2	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-27 
• Released Date: 2017-07-19 
• Deposition Author(s): Kroh, H.K., Chandrasekaran, R., Rosenthal, K., Woods, R., Jin, X., Ohi, M.D., Nyborg, A.C., Rainey, G.J., Warrener, P., Spiller, B.W., Lacy, D.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	AI095755

Revision History 

• Version 1.0: 2017-07-19
  Type: Initial release
• Version 1.1: 2017-07-26
  Type: Author supporting evidence, Database references
• Version 1.2: 2017-09-20
  Type: Database references