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- EMDB-82471: Iota toxin Ib D452A pore -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-82471
TitleIota toxin Ib D452A pore
Map data
Sample
  • Complex: Iota toxin Ib D452A mutant pore
    • Protein or peptide: Iota toxin component Ib
  • Ligand: CALCIUM ION
KeywordsBacterial binary toxin / Protein translocation channel / Toxin
Function / homology
Function and homology information


protein homooligomerization / extracellular region / metal ion binding
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: 2.56 Å
AuthorsYamada T / Nakanishi R / Sugita Y / Ninomiya Y / Yoshida T / Noda T / Tsuge H
Funding support Japan, 5 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
Japan Agency for Medical Research and Development (AMED)6392 Japan
CitationJournal: To Be Published
Title: Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
Authors: Yamada T / Nakanishi R / Sugita Y / Ninomiya Y / Yoshida T / Noda T / Tsuge H
History
DepositionJul 24, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_82471.png

Downloads & links

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Map

FileDownload / File: emd_82471.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å		0.87 Å/pix.
x 320 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.44765854 - 0.7541935
Average (Standard dev.)0.001149644 (±0.01833483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 278.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_82471_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_82471_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 : Iota toxin Ib D452A mutant pore

EntireName: Iota toxin Ib D452A mutant pore
Components
  • Complex: Iota toxin Ib D452A mutant pore
    • Protein or peptide: Iota toxin component Ib
  • Ligand: CALCIUM ION

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Supramolecule #1: Iota toxin Ib D452A mutant pore

SupramoleculeName: Iota toxin Ib D452A mutant pore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridium perfringens (bacteria)

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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)
Molecular weightTheoretical: 58.484211 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EDLDTDNDNI PDAYEKNGYT IKDSIAVKWN DSFAEQGYKK YVSSYLESNT AGDPYTDYQK ASGSIDKAIK LEARDPLVAA YPVVGVGME NLIISTNEHA SSDQGKTVSR ATTNSKTDAN TVGVSISAGY QNGFTGNITT SYSHTTDNST AVQDSNGESW N TGLSINKG ...String:
EDLDTDNDNI PDAYEKNGYT IKDSIAVKWN DSFAEQGYKK YVSSYLESNT AGDPYTDYQK ASGSIDKAIK LEARDPLVAA YPVVGVGME NLIISTNEHA SSDQGKTVSR ATTNSKTDAN TVGVSISAGY QNGFTGNITT SYSHTTDNST AVQDSNGESW N TGLSINKG ESAYINANVR YYNTGTAPMY KVTPTTNLVL DGETLATIKA QDNQIGNNLS PNETYPKKGL SPLALNTMAQ FN ARLIPIN YDQLKKLDSG KQIKLETTQV SGNYGTKNSQ GQIITEGNSW SNYISQIDSV SASIILDTGS QTFERRVAAK EQG NPEDKT PEITIGEAIK KAFSATKNGE LLYFNGIPID ESCVELIFDD NTSEIIKEQL KYLDDKKIYN VKLERGMNIL IKVP SYFTN FDEYNNFPAS WSNIDTKNQD GLQSVANKLS GETKIIIPMS KLKPYKRYVF SGYSKDPSTS NSITVNIKSK EQKTD YLVP EKDYTKFSYE FETTGKDSSD IEITLTSSGV IFLDNLSITE LNSTPE

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: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N204S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMCaCl2calcium chloride
0.003 % (w/v)C47H88022Lauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 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: 4073 / 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: 0.06814 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1990655
CTF correctionSoftware - Name: cryoSPARC (ver. v.4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.5.3) / Number images used: 248921
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v.4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v.4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9jsg


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-44bv:
Iota toxin Ib D452A pore

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