4NP4

Clostridium difficile toxin B CROP domain in complex with FAB domains of neutralizing antibody bezlotoxumab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of Action and Epitopes of Clostridium difficile Toxin B-neutralizing Antibody Bezlotoxumab Revealed by X-ray Crystallography.

Orth, P.Xiao, L.Hernandez, L.D.Reichert, P.Sheth, P.R.Beaumont, M.Yang, X.Murgolo, N.Ermakov, G.DiNunzio, E.Racine, F.Karczewski, J.Secore, S.Ingram, R.N.Mayhood, T.Strickland, C.Therien, A.G.

(2014) J.Biol.Chem. 289: 18008-18021

  • DOI: 10.1074/jbc.M114.560748

  • PubMed Abstract: 
  • The symptoms of Clostridium difficile infections are caused by two exotoxins, TcdA and TcdB, which target host colonocytes by binding to unknown cell surface receptors, at least in part via their combined repetitive oligopeptide (CROP) domains. A com ...

    The symptoms of Clostridium difficile infections are caused by two exotoxins, TcdA and TcdB, which target host colonocytes by binding to unknown cell surface receptors, at least in part via their combined repetitive oligopeptide (CROP) domains. A combination of the anti-TcdA antibody actoxumab and the anti-TcdB antibody bezlotoxumab is currently under development for the prevention of recurrent C. difficile infections. We demonstrate here through various biophysical approaches that bezlotoxumab binds to specific regions within the N-terminal half of the TcdB CROP domain. Based on this information, we solved the x-ray structure of the N-terminal half of the TcdB CROP domain bound to Fab fragments of bezlotoxumab. The structure reveals that the TcdB CROP domain adopts a β-solenoid fold consisting of long and short repeats and that bezlotoxumab binds to two homologous sites within the CROP domain, partially occluding two of the four putative carbohydrate binding pockets located in TcdB. We also show that bezlotoxumab neutralizes TcdB by blocking binding of TcdB to mammalian cells. Overall, our data are consistent with a model wherein a single molecule of bezlotoxumab neutralizes TcdB by binding via its two Fab regions to two epitopes within the N-terminal half of the TcdB CROP domain, partially blocking the carbohydrate binding pockets of the toxin and preventing toxin binding to host cells.


    Organizational Affiliation

    From Merck & Co., Inc., Kenilworth, New Jersey 07023.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toxin B
A
275Clostridioides difficileMutation(s): 0 
Gene Names: toxB (tcdB)
EC: 3.4.22.-
Find proteins for P18177 (Clostridioides difficile)
Go to UniProtKB:  P18177
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
bezlotoxumab heavy chain
H, I
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
bezlotoxumab light chain
L, M
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.413α = 90.00
b = 134.659β = 112.56
c = 102.579γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
SCALAdata scaling
AMoREphasing
JDirectordata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-06-25
    Type: Database references
  • Version 1.2: 2014-07-16
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description