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Yorodumi- PDB-7o43: TrwK/VirB4unbound dimer complex from R388 type IV secretion syste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o43 | |||||||||||||||
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Title | TrwK/VirB4unbound dimer complex from R388 type IV secretion system determined by cryo-EM. | |||||||||||||||
Components | TrwK protein | |||||||||||||||
Keywords | MEMBRANE PROTEIN / type IV secretion system / type 4 secretion system / T4SS / inner membrane complex / inner membrane / R388 plasmid / conjugation / ATPase / bacterial secretion / secretion / secretion system / protein complex / VirB4 / TrwK / dimer / Hcp | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Vadakkepat, A.K. / Mace, K. / Lukoyanova, N. / Waksman, G. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o43.cif.gz | 275.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o43.ent.gz | 221.7 KB | Display | PDB format |
PDBx/mmJSON format | 7o43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o43_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7o43_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7o43_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 7o43_validation.cif.gz | 75.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/7o43 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/7o43 | HTTPS FTP |
-Related structure data
Related structure data | 12717MC 7o3jC 7o3tC 7o3vC 7o41C 7o42C 7oiuC 7q1vC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 94202.328 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: IBA3C:trwM/virB3-trwK/virB4-L6-hcp1C-Strep / Production host: Escherichia coli (E. coli) / References: UniProt: O50330 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hexamer complex of Apo-TrwK/VirB4 with Hcp1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: IBA3C:trwM/virB3-trwK/virB4-L6-hcp1C-Strep |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214048 / Symmetry type: POINT |