8YRM | pdb_00008yrm

Iota toxin Ib pore serine-clamp mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Serine clamp of Clostridium perfringens binary toxin BECb (CPILEb)-pore confers cytotoxicity and enterotoxicity.

Yoshida, T.Monma, C.Ninomiya, Y.Takiguchi, S.Fujita, S.Uchida, Y.Sakoda, N.Karginov, V.A.Kishikawa, J.I.Yamada, T.Kawano, R.Tsuge, H.

(2025) Commun Biol 8: 1102-1102

  • DOI: https://doi.org/10.1038/s42003-025-08519-5
  • Primary Citation of Related Structures:  
    8YRM

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Chemical and Biological Sciences, Japan Women's University, Bunkyo-ku, Tokyo, Japan. yoshidat@fc.jwu.ac.jp.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iota toxin component Ib
A, B, C, D, E
A, B, C, D, E, F, G
528Clostridium perfringensMutation(s): 1 
UniProt
Find proteins for Q46221 (Clostridium perfringens)
Explore Q46221 
Go to UniProtKB:  Q46221
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46221
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
K [auth B]
L [auth C]
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth E],
Q [auth E],
R [auth F],
S [auth F],
T [auth G],
U [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.20.1
MODEL REFINEMENTCoot0.9.8.92

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H02452

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-08-06
    Changes: Data collection, Database references
  • Version 1.3: 2025-08-13
    Changes: Data collection, Database references