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- PDB-9rt2: NetF - ANTXR2 structure (C4) -

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Basic information

Entry
Database: PDB / ID: 9rt2
TitleNetF - ANTXR2 structure (C4)
Components
  • Anthrax toxin receptor 2
  • Leukocidin/Hemolysin toxin family
KeywordsTOXIN / NetF / clostridium perfringens / hemolysin / CMG2 / ANTXR2 / toxin receptor interaction / transmembrane beta-barrel
Function / homology
Function and homology information


cytolysis in another organism / collagen fibril organization / uterus development / Uptake and function of anthrax toxins / single fertilization / transmembrane signaling receptor activity / endosome membrane / external side of plasma membrane / endoplasmic reticulum membrane / cell surface ...cytolysis in another organism / collagen fibril organization / uterus development / Uptake and function of anthrax toxins / single fertilization / transmembrane signaling receptor activity / endosome membrane / external side of plasma membrane / endoplasmic reticulum membrane / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / von Willebrand factor type A domain ...Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Leukocidin/Hemolysin toxin family / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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

Downloads & links

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Assembly

Deposited unit
N1: Leukocidin/Hemolysin toxin family
C1: Anthrax toxin receptor 2
N2: Leukocidin/Hemolysin toxin family
N3: Leukocidin/Hemolysin toxin family
C2: Anthrax toxin receptor 2
N4: Leukocidin/Hemolysin toxin family
N5: Leukocidin/Hemolysin toxin family
C3: Anthrax toxin receptor 2
N6: Leukocidin/Hemolysin toxin family
N7: Leukocidin/Hemolysin toxin family
C4: Anthrax toxin receptor 2
N8: Leukocidin/Hemolysin toxin family


Theoretical massNumber of molelcules
Total (without water)402,91112
Polymers402,91112
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-terminally hexahistidine tagged NetF / Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: netF, JFP838_pC0069 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D3QGV4
#2: Protein
Anthrax toxin receptor 2 / Capillary morphogenesis gene 2 protein / CMG-2


Mass: 34978.652 Da / Num. of mol.: 4 / Mutation: deleted TM and cytoplasmic domains
Source method: isolated from a genetically manipulated source
Details: C-terminally Flag and hexahistidine tagged CMG2ANTXR2
Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR2, CMG2 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P58335
Has protein modificationY

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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: ternary complex of octameric NetF pore with four molecules of ANTXR2/CMG2 (C4)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.418 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: expi293
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: 30000 nm / Nominal defocus min: 10000 nm
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
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67074 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingDetails: modelangelo / Source name: Other / Type: other
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 33.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003626272
ELECTRON MICROSCOPYf_angle_d0.523635583
ELECTRON MICROSCOPYf_chiral_restr0.04363956
ELECTRON MICROSCOPYf_plane_restr0.00294547
ELECTRON MICROSCOPYf_dihedral_angle_d14.32869643

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