44BV | pdb_000044bv

Iota toxin Ib D452A pore

PDB DOI: https://doi.org/10.2210/pdb44BV/pdb
EM Map EMD-82471: EMDB EMDataResource

Classification: TOXIN
Organism(s): Clostridium perfringens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2026-07-24 Released: 2026-08-12
Deposition Author(s): Yamada, T., Nakanishi, R., Sugita, Y., Ninomiya, 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: 2.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Step-by-step maturation mechanism of the binary toxin pore revealed by cryo-EM analysis.

Yamada, T., Nakanishi, R., Sugita, Y., Ninomiya, Y., Yoshida, T., Noda, T., Tsuge, H.

(2026) Proc Natl Acad Sci U S A 123: e2627537123-e2627537123

PubMed: 42804625 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2627537123
Primary Citation Related Structures:
44BV, 44BW

PubMed Abstract:
Membrane pore-forming proteins (PFPs) form ring-shaped membrane-translocating oligomers on membranes, contributing to infection, immunity, and cell death functions. Binary toxins produced by some bacteria consist of an enzymatic component that acts as a toxin and a membrane-binding component that forms a pore that delivers the enzymatic component into target cells. Cryoelectron microscopy (cryo-EM) has advanced our understanding of these translocation mechanisms by revealing several binary toxin complexes' structures. However, the mechanisms underlying the initial pore formation remain unclear. We determined the structures of several oligomeric forms of the membrane-binding component Ib of the iota toxin from Clostridium perfringens at various stages of pore formation. Structural comparisons revealed how the symmetrically arranged soluble oligomer (prepore) asymmetrically matures into a transmembrane oligomer (pore). These findings enhance our understanding of mechanisms of PFP and provide a structural basis for developing nanodevices using membrane pores.

Organizational Affiliation

Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.

Macromolecule Content

Total Structure Weight: 410.23 kDa
Atom Count: 26,957
Modeled Residue Count: 3,451
Deposited Residue Count: 3,710
Unique protein chains: 1

Macromolecules

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| 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	530	Clostridium perfringens	Mutation(s): 1
UniProt
Find proteins for Q46221 (Clostridium perfringens) Explore Q46221 Go to UniProtKB: Q46221
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Z [auth G] SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth G] mmCIF format, chain AA [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: 2.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v.4.5.3
MODEL REFINEMENT	PHENIX	2.0-5936
MODEL REFINEMENT	Coot	0.9.5

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

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
Japan Agency for Medical Research and Development (AMED)	Japan	6392