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- EMDB-61776: Clostridium perfringens iota toxin pore Ib in prepore V state -

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Basic information

Entry
Database: EMDB / ID: EMD-61776
TitleClostridium perfringens iota toxin pore Ib in prepore V state
Map data
Sample
  • Organelle or cellular component: Clostridium perfringens iota toxin component Ib
    • Protein or peptide: Iota toxin component Ib
  • Ligand: CALCIUM ION
KeywordsToxin / Prepore / Pre-pore / Pore / Translocation
Function / homology
Function and homology information


protein homooligomerization / extracellular region
Similarity search - Function
Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 / PA14 domain
Similarity search - Domain/homology
Iota toxin component Ib
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsYamada T / Sugita Y / Yoshida T / Noda T / Tsuge H
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21J13410 Japan
Japan Society for the Promotion of Science (JSPS)21H02452 Japan
Japan Society for the Promotion of Science (JSPS)24K01993 Japan
Japan Agency for Medical Research and Development (AMED)2366 Japan
CitationJournal: To Be Published
Title: Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
Authors: Yamada T / Sugita Y / Yoshida T / Noda T / Tsuge H
History
DepositionSep 30, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61776.png

Downloads & links

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Map

FileDownload / File: emd_61776.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 216 pix.
= 190.08 Å		0.88 Å/pix.
x 216 pix.
= 190.08 Å		0.88 Å/pix.
x 216 pix.
= 190.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.43003523 - 0.97715265
Average (Standard dev.)0.011668787 (±0.08427097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 190.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_61776_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61776_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61776_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Clostridium perfringens iota toxin component Ib

EntireName: Clostridium perfringens iota toxin component Ib
Components
  • Organelle or cellular component: Clostridium perfringens iota toxin component Ib
    • Protein or peptide: Iota toxin component Ib
  • Ligand: CALCIUM ION

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Supramolecule #1: Clostridium perfringens iota toxin component Ib

SupramoleculeName: Clostridium perfringens iota toxin component Ib / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridium perfringens (bacteria) / Strain: NCIB 10748

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Macromolecule #1: Iota toxin component Ib

MacromoleculeName: Iota toxin component Ib / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens (bacteria) / Strain: NCIB 10748
Molecular weightTheoretical: 76.638297 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NNFFDVRFFS AAWEDEDLDT DNDNIPDAYE KNGYTIKDSI AVKWNDSFAE QGYKKYVSSY LESNTAGDPY TDYQKASGSI DKAIKLEAR DPLVAAYPVV GVGMENLIIS TNEHASSDQG KTVSRATTNS KTDANTVGVS ISAGYQNGFT GNITTSYSHT T DNSTAVQD ...String:
NNFFDVRFFS AAWEDEDLDT DNDNIPDAYE KNGYTIKDSI AVKWNDSFAE QGYKKYVSSY LESNTAGDPY TDYQKASGSI DKAIKLEAR DPLVAAYPVV GVGMENLIIS TNEHASSDQG KTVSRATTNS KTDANTVGVS ISAGYQNGFT GNITTSYSHT T DNSTAVQD SNGESWNTGL SINKGESAYI NANVRYYNTG TAPMYKVTPT TNLVLDGETL ATIKAQDNQI GNNLSPNETY PK KGLSPLA LNTMDQFNAR LIPINYDQLK KLDSGKQIKL ETTQVSGNYG TKNSQGQIIT EGNSWSNYIS QIDSVSASII LDT GSQTFE RRVAAKEQGN PEDKTPEITI GEAIKKAFSA TKNGELLYFN GIPIDESCVE LIFDDNTSEI IKEQLKYLDD KKIY NVKLE RGMNILIKVP SYFTNFDEYN NFPASWSNID TKNQDGLQSV ANKLSGETKI IIPMSKLKPY KRYVFSGYSK DPSTS NSIT VNIKSKEQKT DYLVPEKDYT KFSYEFETTG KDSSDIEITL TSSGVIFLDN LSITELNSTP EILKEPEIKV PSDQEI LDA HNKYYADIKL DTNTGNTYID GIYFEPTQTN KEALDYIQKY RVEATLQYSG FKDIGTKDKE IRNYLGDQNQ PKTNYIN FR SYFTSGENVM TYKKLRIYAV TPDNRELLVL SVNLEHHHHH H

UniProtKB: Iota toxin component Ib

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 21 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3tris hydroxymethyl aminomethane
100.0 mMNaClSodium Chloride
1.0 mMCaCl2Calcium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11549 / 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: 0.01 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6223563
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2) / Software - details: patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

0721

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 11285
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)

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Atomic model buiding 1

Initial model
PDB IDChain

6klx

chain_id: ABCD, source_name: PDB, initial_model_type: experimental model

6221

chain_id: EFG, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL
Output model

PDB-9jsl:
Clostridium perfringens iota toxin pore Ib in prepore V state

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