8YRM image
Deposition Date 2024-03-21
Release Date 2025-03-26
Last Version Date 2025-08-13
Entry Detail
PDB ID:
8YRM
Keywords:
Title:
Iota toxin Ib pore serine-clamp mutant
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.36 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Iota toxin component Ib
Mutagens:F454S
Chain IDs:A, B, C, D, E, F, G
Chain Length:528
Number of Molecules:7
Biological Source:Clostridium perfringens
Ligand Molecules
Primary Citation
Serine clamp of Clostridium perfringens binary toxin BECb (CPILEb)-pore confers cytotoxicity and enterotoxicity.
Commun Biol 8 1102 1102 (2025)
PMID: 40715636 DOI: 10.1038/s42003-025-08519-5

Abstact

BEC (CPILE) is a virulence factor of the pathogen, Clostridium perfringens, which has caused foodborne outbreaks in Japan. BEC is a binary toxin that comprises the enzymatic A-component (BECa) and the B-component (BECb); the latter forms a membrane pore to translocate the A-component into target cells. Although BEC differs from other binary toxins in that the B-component alone shows enterotoxic activity, the reason for this remains unclear. We focus on the narrowest region of BECb-pore formed by not phenylalanine residues conserved in other binary toxins including iota toxin B-component (Ib) but serine residues. Comparisons between BECb and BECb (S405F) where the serine residue forming the narrowest region is substituted to the phenylalanine residue reveal that the serine residue is responsible for both cytotoxicity and enterotoxic activity. Though attempts to prepare the BECb-pore were unsuccessful, we reveal the cryo-EM structure of Ib (F454S) where the phenylalanine residue forming the narrowest region is substituted to the serine residue as a surrogate of BECb. Furthermore, Ib (F454S) increases current conductance to nine times that of Ib due to the larger pore diameter and the hydrophilic nature. These results suggest that BECb functions as a pore-forming toxin and as a translocation channel for BECa.

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Chemical

Disease

Primary Citation of related structures
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