5UMI

Clostridium difficile TcdA-CROPs bound to PA50 Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: 10.1074/jbc.M117.781112
  • Primary Citation of Related Structures:  
    5UMI

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toxin AA [auth C]271Clostridioides difficileMutation(s): 0 
Gene Names: toxA, tcdA
EC: 3.4.22 (PDB Primary Data), 2.4.1 (UniProt)
UniProt
Find proteins for P16154 (Clostridioides difficile)
Explore P16154 
Go to UniProtKB:  P16154
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PA50 Fab Light chainD [auth B], B [auth L]211Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PA50 Fab Heavy chainE [auth A], C [auth H]221Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.685α = 90
b = 77.33β = 90.91
c = 97.781γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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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: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence