6OQ6

Structure of the pore forming fragment of Clostridium difficile toxin B in complex with VHH 5D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the full-length Clostridium difficile toxin B.

Chen, P.Lam, K.H.Liu, Z.Mindlin, F.A.Chen, B.Gutierrez, C.B.Huang, L.Zhang, Y.Hamza, T.Feng, H.Matsui, T.Bowen, M.E.Perry, K.Jin, R.

(2019) Nat.Struct.Mol.Biol. 26: 712-719

  • DOI: 10.1038/s41594-019-0268-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clostridium difficile is an opportunistic pathogen that establishes in the colon when the gut microbiota are disrupted by antibiotics or disease. C. difficile infection (CDI) is largely caused by two virulence factors, TcdA and TcdB. Here, we report ...

    Clostridium difficile is an opportunistic pathogen that establishes in the colon when the gut microbiota are disrupted by antibiotics or disease. C. difficile infection (CDI) is largely caused by two virulence factors, TcdA and TcdB. Here, we report a 3.87-Å-resolution crystal structure of TcdB holotoxin that captures a unique conformation of TcdB at endosomal pH. Complementary biophysical studies suggest that the C-terminal combined repetitive oligopeptides (CROPs) domain of TcdB is dynamic and can sample open and closed conformations that may facilitate modulation of TcdB activity in response to environmental and cellular cues during intoxication. Furthermore, we report three crystal structures of TcdB-antibody complexes that reveal how antibodies could specifically inhibit the activities of individual TcdB domains. Our studies provide novel insight into the structure and function of TcdB holotoxin and identify intrinsic vulnerabilities that could be exploited to develop new therapeutics and vaccines for the treatment of CDI.


    Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.,NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, USA.,Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA.,Department of Microbial Pathogenesis, University of Maryland Baltimore, Baltimore, MD, USA.,Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA. r.jin@uci.edu.,Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toxin B
A
363Clostridioides 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
5D
D
153N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.259 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 169.820α = 90.00
b = 169.820β = 90.00
c = 79.120γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States--

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references
  • Version 1.2: 2019-08-21
    Type: Data collection, Database references
  • Version 1.3: 2019-12-04
    Type: Author supporting evidence