5VQM

Clostridium difficile TcdB-GTD bound to PA41 Fab


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M117.813428

  • PubMed Abstract: 
  • Clostridium difficile infection (CDI) 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 multi-step process of receptor binding, endocytosis, ...

    Clostridium difficile infection (CDI) 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 multi-step process of receptor binding, endocytosis, low pH-induced pore formation, and the translocation and delivery of an N-terminal glucosyltransferase domain (GTD) 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 CDI 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 GTD 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.


    Organizational Affiliation

    Vanderbilt University Medical Center, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toxin B
A, B
557Peptoclostridium difficile (strain R20291)Mutation(s): 0 
Gene Names: tcdB
Find proteins for C9YJ35 (Peptoclostridium difficile (strain R20291))
Go to UniProtKB:  C9YJ35
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PA41 FAB LIGHT CHAIN
L, C
214Homo sapiensMutation(s): 0 
Find proteins for Q8TCD0 (Homo sapiens)
Go to UniProtKB:  Q8TCD0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PA41 FAB HEAVY CHAIN
H, D
222Homo sapiensMutation(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 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 96.130α = 90.00
b = 251.740β = 90.00
c = 224.450γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI095755

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-31
    Type: Database references