9JSF | pdb_00009jsf

Clostridium perfringens iota toxin pore Ib in prepore I state

• PDB DOI: https://doi.org/10.2210/pdb9JSF/pdb
• EM Map EMD-61771: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-30 Released: 2025-05-14 
• Deposition Author(s): Yamada, T., Sugita, Y., Yoshida, T., Noda, T., Tsuge, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis

Yamada, T., Sugita, Y., Yoshida, T., Noda, T., Tsuge, H.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 58.89 kDa 
• Atom Count: 3,919 
• Modeled Residue Count: 509 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iota toxin component Ib	A	532	Clostridium perfringens	Mutation(s): 0
UniProt
Find proteins for Q46221 (Clostridium perfringens) Explore Q46221  Go to UniProtKB:  Q46221

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2
MODEL REFINEMENT	Coot	0.9.5
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Yamada, T., Sugita, Y., Yoshida, T., Noda, T., Tsuge, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21J13410
Japan Society for the Promotion of Science (JSPS)	Japan	21H02452
Japan Society for the Promotion of Science (JSPS)	Japan	24K01993
Japan Agency for Medical Research and Development (AMED)	Japan	2366

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release