6OQ7 | pdb_00006oq7

Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH E3

• PDB DOI: https://doi.org/10.2210/pdb6OQ7/pdb

• Classification: TOXIN
• Organism(s): Clostridioides difficile, Camelidae
• Expression System: Priestia megaterium, Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-25 Released: 2019-07-10 
• Deposition Author(s): Chen, P., Lam, K., Jin, R.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

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

• PubMed: 31308519 
• DOI: https://doi.org/10.1038/s41594-019-0268-0
• Primary Citation Related Structures: 
  6OQ5, 6OQ6, 6OQ7, 6OQ8


• 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 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.

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Organizational Affiliation: 
• Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.
Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA.
Department of Microbial Pathogenesis, University of Maryland Baltimore, Baltimore, MD, USA.
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, University of California, Irvine, Irvine, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.94 kDa 
• Atom Count: 5,368 
• Modeled Residue Count: 650 
• Deposited Residue Count: 686 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin B	A	549	Clostridioides difficile	Mutation(s): 0  Gene Names: tcdB EC: 3.4.22
UniProt
Find proteins for Q9EXR0 (Clostridioides difficile) Explore Q9EXR0  Go to UniProtKB:  Q9EXR0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3	B [auth C]	137	Camelidae	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	C [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
GLC	D [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MN	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.018	α = 90
b = 104.096	β = 90
c = 113.825	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Chen, P., Lam, K., Jin, R.

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Funding Organization	Location	Grant 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
  Changes: Data collection, Database references
• Version 1.2: 2019-08-21
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.6: 2024-10-23
  Changes: Structure summary