9MUI

C. difficile RBD1 with Ca2+

Summary for 9MUI

• Entry DOI: 10.2210/pdb9mui/pdb
• Descriptor: ADP-ribosyltransferase binding component, CALCIUM ION (3 entities in total)
• Functional Keywords: c. difficile, rbd1, calcium, cdtb rbd1, toxin
• Biological source: Clostridioides difficile
• Total number of polymer chains: 4
• Total formula weight: 58027.87

Authors

Hunter, D.,Pozharski, E. (deposition date: 2025-01-14, release date: 2025-08-20)

Primary citation

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.
Pore formation by the CDTb component of the Clostridioides difficile binary toxin is Ca 2+ -dependent.
Commun Biol, 8:901-901, 2025

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 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 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-binding double mutant targeting RBD1 (i.e., D623A/D734A) support a model in which dissociation of Ca from RBD1 induces dynamic properties in CDTb that enable it to bind and form pores in lipid bilayers.

PubMed: 40490540
DOI: 10.1038/s42003-025-08343-x

Experimental method

X-RAY DIFFRACTION (2.29 Å)