9JSI | pdb_00009jsi

Clostridium perfringens iota toxin pore Ib in prepore II state

PDB DOI: https://doi.org/10.2210/pdb9JSI/pdb
EM Map EMD-61774: 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 537.31 kDa
Atom Count: 26,595
Modelled Residue Count: 3,453
Deposited Residue Count: 4,781
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iota toxin component Ib	A, B, C, D, E A, B, C, D, E, F, G	683	Clostridium perfringens	Mutation(s): 0
UniProt
Find proteins for Q46221 (Clostridium perfringens) Explore Q46221 Go to UniProtKB: Q46221
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46221
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth G]	AA [auth G] BA [auth G] H [auth A] I [auth A] J [auth A] AA [auth G], BA [auth G], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth D], R [auth D], S [auth D], T [auth E], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth F], Z [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

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