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- PDB-6rwb: Cryo-EM structure of Yersinia pseudotuberculosis TcaA-TcaB -

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Entry
Database: PDB / ID: 6rwb
TitleCryo-EM structure of Yersinia pseudotuberculosis TcaA-TcaB
ComponentsToxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit
KeywordsTOXIN / membrane permeation / translocation / complex
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsRoderer, D. / Leidreiter, F. / Gatsogiannis, C. / Meusch, D. / Benz, R. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Sci Adv / Year: 2019
Title: Common architecture of Tc toxins from human and insect pathogenic bacteria.
Authors: F Leidreiter / D Roderer / D Meusch / C Gatsogiannis / R Benz / S Raunser /
Abstract: Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution ...Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family.
History
DepositionJun 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

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Assembly

Deposited unit
A: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit
B: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit
C: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit
D: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit
E: Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit


Theoretical massNumber of molelcules
Total (without water)1,159,9255
Polymers1,159,9255
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area119710 Å2
ΔGint-354 kcal/mol
Surface area400270 Å2
MethodPISA

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Components

#1: Protein
Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit


Mass: 231985.031 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: EGX47_10580, YPP3681, NCTC8580_04191 / Production host: Escherichia coli (E. coli) / Variant (production host): RIPL

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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: Y. pseudotuberculosis TcaA-TcaB pentamer / Type: COMPLEX / Details: Each protomer is a fusion protein of TcaA and TcaB / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Yersinia pseudotuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 130 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
9PHENIXmodel refinement
10SPHIREinitial Euler assignment
11SPHIREfinal Euler assignment
13SPHIRE3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237295 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1VW1

1vw1
PDB Unreleased entry


Accession code: 1VW1 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00676915
ELECTRON MICROSCOPYf_angle_d0.971104180
ELECTRON MICROSCOPYf_dihedral_angle_d7.89946615
ELECTRON MICROSCOPYf_chiral_restr0.05411525
ELECTRON MICROSCOPYf_plane_restr0.00713555

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