Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 223.37 kDa 
• Atom Count: 15298 
• Residue Count: 1916 
• Unique protein chains: 3

5VQM

Clostridium difficile TcdB-GTD bound to PA41 Fab

• DOI: 10.2210/pdb5VQM/pdb

• Classification: TOXIN/IMMUNE SYSTEM
• Organism(s): Clostridioides difficile R20291, Homo sapiens
• Expression System: Bacillus megaterium, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2017-05-09 Released: 2017-12-06 
• Deposition Author(s): Kroh, H.K., Spiller, B.W., Lacy, D.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

Literature

A neutralizing antibody that blocks delivery of the enzymatic cargo of Clostridium difficile toxin TcdB into host cells.

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

(2018) J Biol Chem 293: 941-952

• PubMed: 29180448 
• DOI: 10.1074/jbc.M117.813428
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Clostridium difficile infection is the leading cause of hospital-acquired diarrhea and is mediated by the actions of two toxins, TcdA and TcdB. The toxins perturb host cell function through a multistep process of receptor binding, endocytosis, low pH-induced pore formation, and the translocation and delivery of an N-terminal glucosyltransferase domain that inactivates host GTPases. Infection studies with isogenic strains having defined toxin deletions have established TcdB as an important target for therapeutic development. Monoclonal antibodies that neutralize TcdB function have been shown to protect against C. difficile infection in animal models and reduce recurrence in humans. Here, we report the mechanism of TcdB neutralization by PA41, a humanized monoclonal antibody capable of neutralizing TcdB from a diverse array of C. difficile strains. Through a combination of structural, biochemical, and cell functional studies, involving X-ray crystallography and EM, we show that PA41 recognizes a single, highly conserved epitope on the TcdB glucosyltransferase domain and blocks productive translocation and delivery of the enzymatic cargo into the host cell. Our study reveals a unique mechanism of C. difficile toxin neutralization by a monoclonal antibody, which involves targeting a process that is conserved across the large clostridial glucosylating toxins. The PA41 antibody described here provides a valuable tool for dissecting the mechanism of toxin pore formation and translocation across the endosomal membrane.

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Organizational Affiliation: 

Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37212-2637.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Toxin B	A, B	557	Clostridioides difficile R20291	Mutation(s): 0  Gene Names: tcdB, CDR20291_0582
Find proteins for C9YJ35 (Clostridioides difficile (strain R20291)) Go to UniProtKB:  C9YJ35

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PA41 FAB LIGHT CHAIN	C, L	214	Homo sapiens	Mutation(s): 0
Find proteins for Q8TCD0 (Homo sapiens) Go to UniProtKB:  Q8TCD0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PA41 FAB HEAVY CHAIN	D, H	222	Homo sapiens	Mutation(s): 0
Find proteins for S6B291 (Homo sapiens) Go to UniProtKB:  S6B291

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.13	α = 90
b = 251.74	β = 90
c = 224.45	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-09 
• Released Date: 2017-12-06 
Deposition Author(s): Kroh, H.K., 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 (NIH/NIAID)	United States	AI095755

Revision History 

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence