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- EMDB-64005: Iota toxin Ib pore serine-clamp mutant(C1) -

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Basic information

Entry
Database: EMDB / ID: EMD-64005
TitleIota toxin Ib pore serine-clamp mutant(C1)
Map data
Sample
  • Complex: Iota toxin Ib pore serine-clamp mutant(C1)
KeywordsBacterial binary toxin / Protein translocation channel / ADP-ribosylation / Toxin
Biological speciesClostridium perfringens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsNinomiya Y / Yoshida T / Yamada T / Kishikawa J / Tsuge H
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02452 Japan
CitationJournal: Commun Biol / Year: 2025
Title: Serine clamp of Clostridium perfringens binary toxin BECb (CPILEb)-pore confers cytotoxicity and enterotoxicity.
Authors: Toru Yoshida / Chie Monma / Yuki Ninomiya / Sotaro Takiguchi / Shoko Fujita / Yuto Uchida / Noriaki Sakoda / Vladimir A Karginov / Jun-Ichi Kishikawa / Tomohito Yamada / Ryuji Kawano / Hideaki Tsuge /
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 ...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.
History
DepositionApr 3, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64005.png

Downloads & links

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Map

FileDownload / File: emd_64005.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 360 pix.
= 243. Å		0.68 Å/pix.
x 360 pix.
= 243. Å		0.68 Å/pix.
x 360 pix.
= 243. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.23189601 - 0.70478123
Average (Standard dev.)0.0045804544 (±0.031753473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64005_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_64005_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_64005_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Iota toxin Ib pore serine-clamp mutant(C1)

EntireName: Iota toxin Ib pore serine-clamp mutant(C1)
Components
  • Complex: Iota toxin Ib pore serine-clamp mutant(C1)

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Supramolecule #1: Iota toxin Ib pore serine-clamp mutant(C1)

SupramoleculeName: Iota toxin Ib pore serine-clamp mutant(C1) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Clostridium perfringens (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.669 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4S2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid
1.0 mMCaCl2calcium chloride
0.003 % (w/v)C47H88O22Lauryl Maltose Neopentyl Glycol

Details: 10mM HEPES pH 7.5, 1mM CaCl2, 0.003% (w/v) LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7080 / Average exposure time: 2.89 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0938 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1379432
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2) / Software - details: Patch CTF estimation (multi) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-uniform refinement / Number images used: 354215
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 150 / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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