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- PDB-9rsu: NetF pore structure -

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Basic information

Entry
Database: PDB / ID: 9rsu
TitleNetF pore structure
ComponentsLeukocidin/Hemolysin toxin family
KeywordsTOXIN / pore forming toxin / hemolysin / clostridium perfringens / transmembrane pore / beta-barrel.
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsWang, C. / Iacovache, I. / Zuber, B.
Funding support Switzerland, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocidin/Hemolysin toxin family
B: Leukocidin/Hemolysin toxin family
C: Leukocidin/Hemolysin toxin family
D: Leukocidin/Hemolysin toxin family
E: Leukocidin/Hemolysin toxin family
F: Leukocidin/Hemolysin toxin family
G: Leukocidin/Hemolysin toxin family
H: Leukocidin/Hemolysin toxin family


Theoretical massNumber of molelcules
Total (without water)262,9978
Polymers262,9978
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Leukocidin/Hemolysin toxin family / Necrotizing enteritis toxin NetF


Mass: 32874.590 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tagged NetF / Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: netF, JFP838_pC0069 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D3QGV4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NetF / Type: COMPLEX
Details: 8mer NetF pore solubilized from liposomes in DDM:CHS
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 33 kDa/nm / Experimental value: NO
Source (natural)Organism: Clostridium perfringens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris bufferTris1
2150 mMsodium chlorideNaCl1
31 mMDithiothreitolDTT1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: solubilized and monodisperse in DDM:CHS
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
7PHENIXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278866 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: Modelangelo was used to generate the initial model
Atomic model buildingDetails: modelangelo / Source name: Other / Type: other
RefinementHighest resolution: 2.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417664
ELECTRON MICROSCOPYf_angle_d0.42723944
ELECTRON MICROSCOPYf_dihedral_angle_d4.2172352
ELECTRON MICROSCOPYf_chiral_restr0.0412576
ELECTRON MICROSCOPYf_plane_restr0.0033056

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