9MUI | pdb_00009mui

C. difficile RBD1 with Ca2+

• PDB DOI: https://doi.org/10.2210/pdb9MUI/pdb

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


• Deposited: 2025-01-14 Released: 2025-08-20 
• Deposition Author(s): Hunter, D., Pozharski, E.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Pore formation by the CDTb component of the Clostridioides difficile binary toxin is Ca 2+ -dependent.

Abeyawardhane, D.L., Sevdalis, S.E., Adipietro, K.A., Godoy-Ruiz, R., Varney, K.M., Nawaz, I.F., Spittel, A.X., Hunter, D., Rustandi, R.R., Silin, V.I., des Georges, A., Cook, M.E., Pozharski, E., Weber, D.J.

(2025) Commun Biol 8: 901-901

• PubMed: 40490540 
• DOI: https://doi.org/10.1038/s42003-025-08343-x
• Primary Citation of Related Structures:  
  9MUI


• PubMed Abstract: 
  

  Clostridioides difficile infection (CDI) is one of the five most urgent bacterial threats in the United States. Furthermore, hypervirulent CDI strains express a third toxin termed the C. difficile binary toxin (CDT), and its molecular mechanism for entering host cells is not fully elucidated. Like other AB-type binary toxins, CDT enters host cells via endosomes. Here we show via surface plasmon resonance and electrochemical impedance spectroscopy that the cell-binding component of CDT, termed CDTb, binds and form pores in lipid bilayers in the absence of its enzymatic component, CDTa. This occurs upon lowering free Ca ²⁺ ion concentration, and not by decreasing pH, as found for other binary toxins (i.e., anthrax). Cryogenic electron microscopy (CryoEM), X-ray crystallography, and nuclear magnetic resonance (NMR) studies show that dissociation of Ca ²⁺ from a single site in receptor binding domain 1 (RBD1) of CDTb triggers conformational exchange in CDTb. These and structure/function studies of a Ca ²⁺ -binding double mutant targeting RBD1 (i.e., D623A/D734A) support a model in which dissociation of Ca ²⁺ from RBD1 induces dynamic properties in CDTb that enable it to bind and form pores in lipid bilayers.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA.
The Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD, USA.
Merck & Co. Inc., Kenilworth, NJ, USA.
National Institute of Standards and Technology, Gaithersburg, MD, USA.
Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA.
Department of Chemistry and Biochemistry, City College of New York, New York, NY, USA.
PhD Programs in Biochemistry and Chemistry, Graduate Center, City University of New York, New York, NY, USA.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA. [e-mail].
Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA. [e-mail].
The Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD, USA. [e-mail].
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA. [e-mail].
Institute for Bioscience and Biotechnology Research (IBBR), University of Maryland, Rockville, MD, USA. [e-mail].
The Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.03 kDa 
• Atom Count: 4,260 
• Modeled Residue Count: 508 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyltransferase binding component	A, B, C, D	127	Clostridioides difficile	Mutation(s): 0  Gene Names: cdtB
UniProt
Find proteins for A8DS70 (Clostridioides difficile) Explore A8DS70  Go to UniProtKB:  A8DS70

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.697	α = 90
b = 119.697	β = 90
c = 125.091	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Hunter, D., Pozharski, E.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release