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- PDB-8rta: Arches-protomer complex full-length structure (TrwJ/VirB8) from t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rta | |||||||||||||||
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Title | Arches-protomer complex full-length structure (TrwJ/VirB8) from the fully-assembled R388 type IV secretion system determined by cryo-EM. | |||||||||||||||
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![]() | MEMBRANE PROTEIN / type IV secretion system type 4 secretion system T4SS Arches Arches-protomer R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB8 VirB10 TrwG TrwE | |||||||||||||||
Function / homology | ![]() protein secretion by the type IV secretion system / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.22 Å | |||||||||||||||
![]() | Mace, K. / Waksman, G. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of a conjugative type IV secretion system suggests a molecular switch regulating pilus biogenesis. Authors: Kévin Macé / Gabriel Waksman / ![]() ![]() Abstract: Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. ...Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. Bacterial conjugation is the primary means by which antibiotic resistance genes spread among bacterial populations (Barlow 2009; Virolle et al, 2020). Conjugative T4SSs form pili: long extracellular filaments that connect with recipient cells. Previously, we solved the cryo-electron microscopy (cryo-EM) structure of a conjugative T4SS. In this article, based on additional data, we present a more complete T4SS cryo-EM structure than that published earlier. Novel structural features include details of the mismatch symmetry within the OMCC, the presence of a fourth VirB8 subunit in the asymmetric unit of both the arches and the inner membrane complex (IMC), and a hydrophobic VirB5 tip in the distal end of the stalk. Additionally, we provide previously undescribed structural insights into the protein VirB10 and identify a novel regulation mechanism of T4SS-mediated pilus biogenesis by this protein, that we believe is a key checkpoint for this process. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.8 KB | Display | ![]() |
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PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 19484MC ![]() 8rt4C ![]() 8rt5C ![]() 8rt6C ![]() 8rt7C ![]() 8rt8C ![]() 8rt9C ![]() 8rtbC ![]() 8rtdC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 25799.994 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 42443.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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Sample preparation
Component | Name: Arches-protomer complex from the fully-assembled R388 type IV secretion system Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 3300 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 57.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 6.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115034 / Symmetry type: POINT |