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- PDB-7o3v: Stalk complex structure (TrwJ/VirB5-TrwI/VirB6) from the fully-as... -

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Basic information

Entry
Database: PDB / ID: 7o3v
TitleStalk complex structure (TrwJ/VirB5-TrwI/VirB6) from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Components
  • TrwI protein
  • TrwJ protein
KeywordsMEMBRANE PROTEIN / type IV secretion system / type 4 secretion system / T4SS / stalk / stalk complex / inner membrane / R388 plasmid / conjugation / bacterial secretion / secretion / secretion system / protein complex / VirB5 / VirB6 / TrwJ / TrwI
Function / homologyType IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Plasmid conjugal transfer TrbL/VirB6 / TrbL/VirB6 plasmid conjugal transfer protein / protein secretion by the type IV secretion system / membrane / TrwJ protein / TrwI protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMace, K. / Vadakkepat, A.K. / Lukoyanova, N. / Waksman, G.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
Wellcome Trust217089 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nature / Year: 2022
Title: Cryo-EM structure of a type IV secretion system.
Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong ...Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman /
Abstract: Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
History
DepositionApr 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TrwJ protein
B: TrwJ protein
C: TrwJ protein
D: TrwJ protein
E: TrwJ protein
F: TrwI protein
G: TrwI protein
H: TrwI protein
I: TrwI protein
J: TrwI protein


Theoretical massNumber of molelcules
Total (without water)302,57310
Polymers302,57310
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area71080 Å2
ΔGint-487 kcal/mol
Surface area90470 Å2
MethodPISA

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Components

#1: Protein
TrwJ protein


Mass: 25190.461 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwJ
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB/virD4
Production host: Escherichia coli (E. coli) / References: UniProt: O50331
#2: Protein
TrwI protein


Mass: 35324.172 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwI
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB/virD4
Production host: Escherichia coli (E. coli) / References: UniProt: O50333

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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: Type IV secretion system complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.808 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: R388 plasmid
Source (recombinant)Organism: Escherichia coli (E. coli)
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB /virD4
Buffer solutionpH: 7.6
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: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 57.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 566815 / Symmetry type: POINT

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