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 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1074/jbc.M117.813428
  • Primary Citation of Related Structures:  
    5VQM

  • 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin BA,
D [auth B]
557Clostridioides difficile R20291Mutation(s): 0 
Gene Names: tcdBCDR20291_0582
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PA41 FAB LIGHT CHAINB [auth L],
E [auth C]
214Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
Entity Groups  
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UniProt GroupQ8TCD0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PA41 FAB HEAVY CHAINC [auth H],
F [auth D]
222Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B291 (Homo sapiens)
Explore S6B291 
Go to UniProtKB:  S6B291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6B291
Sequence Annotations
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  • Reference Sequence
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 = 96.13α = 90
b = 251.74β = 90
c = 224.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI095755

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description