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- EMDB-54221: NetF 9mer pre-pore map on 2N2 nanodiscs. -

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Basic information

Entry
Database: EMDB / ID: EMD-54221
TitleNetF 9mer pre-pore map on 2N2 nanodiscs.
Map data
Sample
  • Complex: pre-pore of NetF in 9mer conformation.
    • Protein or peptide: Leukocidin/Hemolysin toxin family
Keywordspore forming toxin / hemolysin / clostridium perfringens / pre-pore. / 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: 2.13 Å
AuthorsIacovache I / Wang C / 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 / 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_54221.png

Downloads & links

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Map

FileDownload / File: emd_54221.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.12655051 - 0.38483196
Average (Standard dev.)0.00094154634 (±0.01402299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_54221_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54221_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_54221_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 : pre-pore of NetF in 9mer conformation.

EntireName: pre-pore of NetF in 9mer conformation.
Components
  • Complex: pre-pore of NetF in 9mer conformation.
    • Protein or peptide: Leukocidin/Hemolysin toxin family

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Supramolecule #1: pre-pore of NetF in 9mer conformation.

SupramoleculeName: pre-pore of NetF in 9mer conformation. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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-terminally his tagged NetF / Number of copies: 9 / 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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: cryosparc ab-inition 100000 particles
Final reconstructionNumber classes used: 7 / Applied symmetry - Point group: C9 (9 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1088311
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
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 get an initial model.
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9rsm:
NetF 9mer pre-pore structure on 2N2 nanodiscs.

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