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- EMDB-54226: NetF pore structure -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54226
TitleNetF pore structure
Map datamap
Sample
  • Complex: NetF
    • Protein or peptide: Leukocidin/Hemolysin toxin family
Keywordspore forming toxin / hemolysin / clostridium perfringens / transmembrane pore / beta-barrel. / TOXIN
Function / homologyBi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / cytolysis in another organism / extracellular region / Leukocidin/Hemolysin toxin family
Function and homology information
Biological speciesClostridium perfringens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsWang C / Iacovache I / Zuber B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation10000175 Switzerland
CitationJournal: To Be Published
Title: Anthrax toxin receptor 2 is the Receptor for Clostridium perfringens NetF: Structural Insights into Toxin Binding and Pore Formation
Authors: Wang C / Cattalani F / Iacovache I / Arunasalam N / Posthaus H / Zuber B
History
DepositionJul 1, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54226.png

Downloads & links

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Map

FileDownload / File: emd_54226.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 263.52 Å		0.73 Å/pix.
x 360 pix.
= 263.52 Å		0.73 Å/pix.
x 360 pix.
= 263.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.14050782 - 0.39004052
Average (Standard dev.)0.0010753964 (±0.015086875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 263.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharp map

Fileemd_54226_additional_1.map
Annotationsharp map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_54226_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_54226_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NetF

EntireName: NetF
Components
  • Complex: NetF
    • Protein or peptide: Leukocidin/Hemolysin toxin family

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Supramolecule #1: NetF

SupramoleculeName: NetF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 8mer NetF pore solubilized from liposomes in DDM:CHS
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 33 kDa/nm

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Macromolecule #1: Leukocidin/Hemolysin toxin family

MacromoleculeName: Leukocidin/Hemolysin toxin family / type: protein_or_peptide / ID: 1 / Details: N-terminal hexahistidine tagged NetF / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens (bacteria)
Molecular weightTheoretical: 32.87459 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVHHHHHHNS FPESIINSKG KQAEVYTSSD ASERDGIKTS LSASFIEDPN SNNLTALVSL KGFIPSGLIK TGTYYSANMY WPSKYNINI ETTDEKNNVK ILESIPSNTI ETVRVTESMG YSIGGNVSVS KKSSSVGANA GFNVQRSVQY EQPDFKTIQK S DGIRKASW ...String:
MVHHHHHHNS FPESIINSKG KQAEVYTSSD ASERDGIKTS LSASFIEDPN SNNLTALVSL KGFIPSGLIK TGTYYSANMY WPSKYNINI ETTDEKNNVK ILESIPSNTI ETVRVTESMG YSIGGNVSVS KKSSSVGANA GFNVQRSVQY EQPDFKTIQK S DGIRKASW NIVFNKTKDG YDQNSYHALY GNQLFMKSRL HNTGAKNLVE DKDLSPLISG GFTPNMVIAL KAPKGTKKSM IN LNYNLYQ DLYTLEWYKT QWWGENRVAK EPYYTYQTYE LDWENHTVEF IY

UniProtKB: Leukocidin/Hemolysin toxin family

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris buffer
150.0 mMNaClsodium chloride
1.0 mMDTTDithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Detailssolubilized and monodisperse in DDM:CHS

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: cryosparct ab-initio
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 278866
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC / Details: cryosparc refine
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: modelangelo
DetailsModelangelo was used to generate the initial model
RefinementProtocol: OTHER
Output model

PDB-9rsu:
NetF pore structure

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