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- PDB-7q9y: Cryo-EM structure of the octameric pore of Clostridium perfringen... -

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Basic information

Entry
Database: PDB / ID: 7q9y
TitleCryo-EM structure of the octameric pore of Clostridium perfringens beta-toxin.
ComponentsClostridium perfringens beta toxin
KeywordsTOXIN / pore forming toxin / hemolysin / octamer
Function / homologyLeukocidin/porin MspA / Leukocidin-like / Distorted Sandwich / Mainly Beta
Function and homology information
Biological speciesClostridium perfringens CPE (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsIacovache, I. / Zuber, B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation179520 Switzerland
CitationJournal: EMBO Rep / Year: 2022
Title: Cryo-EM structure of the octameric pore of Clostridium perfringens β-toxin.
Authors: Julia Bruggisser / Ioan Iacovache / Samuel C Musson / Matteo T Degiacomi / Horst Posthaus / Benoît Zuber /
Abstract: Clostridium perfringens is one of the most widely distributed and successful pathogens producing an impressive arsenal of toxins. One of the most potent toxins produced is the C. perfringens β-toxin ...Clostridium perfringens is one of the most widely distributed and successful pathogens producing an impressive arsenal of toxins. One of the most potent toxins produced is the C. perfringens β-toxin (CPB). This toxin is the main virulence factor of type C strains. We describe the cryo-electron microscopy (EM) structure of CPB oligomer. We show that CPB forms homo-octameric pores like the hetero-oligomeric pores of the bi-component leukocidins, with important differences in the receptor binding region and the N-terminal latch domain. Intriguingly, the octameric CPB pore complex contains a second 16-stranded β-barrel protrusion atop of the cap domain that is formed by the N-termini of the eight protomers. We propose that CPB, together with the newly identified Epx toxins, is a member a new subclass of the hemolysin-like family. In addition, we show that the β-barrel protrusion domain can be modified without affecting the pore-forming ability, thus making the pore particularly attractive for macromolecule sensing and nanotechnology. The cryo-EM structure of the octameric pore of CPB will facilitate future developments in both nanotechnology and basic research.
History
DepositionNov 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Data collection / Database references
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clostridium perfringens beta toxin
B: Clostridium perfringens beta toxin
C: Clostridium perfringens beta toxin
D: Clostridium perfringens beta toxin
E: Clostridium perfringens beta toxin
F: Clostridium perfringens beta toxin
G: Clostridium perfringens beta toxin
H: Clostridium perfringens beta toxin


Theoretical massNumber of molelcules
Total (without water)279,1508
Polymers279,1508
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33860 Å2
ΔGint-109 kcal/mol
Surface area105360 Å2

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Components

#1: Protein
Clostridium perfringens beta toxin


Mass: 34893.750 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens CPE (bacteria) / Gene: beta toxin / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: octamer of beta toxin in SMALP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Clostridium perfringens (bacteria) / Strain: C
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
120 mMTris1
2150 mMNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm / Cs: 2.25 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 80 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260481 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 3B07

3b07


Pdb chain-ID: B / Accession code: 3B07 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00716152
ELECTRON MICROSCOPYf_angle_d0.88922096
ELECTRON MICROSCOPYf_dihedral_angle_d6.6362368
ELECTRON MICROSCOPYf_chiral_restr0.0542648
ELECTRON MICROSCOPYf_plane_restr0.0062808

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