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- PDB-7o41: Hexameric composite model of the Inner Membrane Complex (IMC) wit... -

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Basic information

Entry
Database: PDB / ID: 7o41
TitleHexameric composite model of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Components
  • TrwG protein
  • TrwK protein
  • TrwM protein
KeywordsMEMBRANE PROTEIN / type IV secretion system / type 4 secretion system / T4SS / IMC / inner membrane complex / inner membrane / arches / periplasmic / R388 plasmid / conjugation / bacterial secretion / secretion / secretion system / protein complex / VirB3 / VirB4 / VirB8 / TrwM / TrwK / TrwG
Function / homology
Function and homology information


protein secretion by the type IV secretion system / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Type IV secretion system, VirB3 / TrbD / AvhB / Type IV secretory pathway, VirB3-like protein / CagE, TrbE, VirB component of type IV transporter system, central domain / CagE, TrbE, VirB family, component of type IV transporter system / CagE, TrbE, VirB component of type IV transporter system / TraG, P-loop domain / TraG P-loop domain / Type IV secretion system protein VirB8/PtlE / : / Bacterial virulence protein VirB8 ...Type IV secretion system, VirB3 / TrbD / AvhB / Type IV secretory pathway, VirB3-like protein / CagE, TrbE, VirB component of type IV transporter system, central domain / CagE, TrbE, VirB family, component of type IV transporter system / CagE, TrbE, VirB component of type IV transporter system / TraG, P-loop domain / TraG P-loop domain / Type IV secretion system protein VirB8/PtlE / : / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TrwM protein / Type IV secretion system protein virB4 / TrwG protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 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 4, 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
C: TrwM protein
A: TrwK protein
B: TrwK protein
D: TrwG protein
E: TrwG protein
F: TrwG protein


Theoretical massNumber of molelcules
Total (without water)277,2326
Polymers277,2326
Non-polymers00
Water00
1
C: TrwM protein
A: TrwK protein
B: TrwK protein
D: TrwG protein
E: TrwG protein
F: TrwG protein
x 6


Theoretical massNumber of molelcules
Total (without water)1,663,39536
Polymers1,663,39536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
identity operation1_555x,y,z1

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Components

#1: Protein TrwM protein


Mass: 12292.585 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwM
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB/virD4
Production host: Escherichia coli (E. coli) / References: UniProt: O50329
#2: Protein TrwK protein


Mass: 93769.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwK
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB/virD4
Production host: Escherichia coli (E. coli) / References: UniProt: O50330
#3: Protein TrwG protein


Mass: 25799.994 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwG
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB/virD4
Production host: Escherichia coli (E. coli) / References: UniProt: O50335

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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
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126975 / Symmetry type: POINT

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