9MUI image
Deposition Date 2025-01-14
Release Date 2025-08-20
Last Version Date 2025-08-20
Entry Detail
PDB ID:
9MUI
Keywords:
Title:
C. difficile RBD1 with Ca2+
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.29 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
H 3
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ADP-ribosyltransferase binding component
Gene (Uniprot):cdtB
Chain IDs:A, B, C, D
Chain Length:127
Number of Molecules:4
Biological Source:Clostridioides difficile
Ligand Molecules
Primary Citation
Pore formation by the CDTb component of the Clostridioides difficile binary toxin is Ca 2+ -dependent.
Commun Biol 8 901 901 (2025)
PMID: 40490540 DOI: 10.1038/s42003-025-08343-x

Abstact

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 Ca2+ 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 Ca2+ from a single site in receptor binding domain 1 (RBD1) of CDTb triggers conformational exchange in CDTb. These and structure/function studies of a Ca2+-binding double mutant targeting RBD1 (i.e., D623A/D734A) support a model in which dissociation of Ca2+ from RBD1 induces dynamic properties in CDTb that enable it to bind and form pores in lipid bilayers.

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Chemical

Disease

Primary Citation of related structures
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