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Yorodumi- PDB-8rta: Arches-protomer complex full-length structure (TrwJ/VirB8) from t... -
+Open data
-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. | |||||||||||||||
Components |
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Keywords | 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 | Function and homology information protein secretion by the type IV secretion system / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.22 Å | |||||||||||||||
Authors | Mace, K. / Waksman, G. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: To Be Published / Year: 2024 Title: Cryo-EM structure of a conjugative type 4 secretion system identifies a molecular switch regulating conjugative pilus biogenesis Authors: Mace, K. / Waksman, G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rta.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rta.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 8rta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rta_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8rta_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8rta_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 8rta_validation.cif.gz | 60.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/8rta ftp://data.pdbj.org/pub/pdb/validation_reports/rt/8rta | HTTPS FTP |
-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 (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: 25799.994 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwG / Production host: Escherichia coli (E. coli) / References: UniProt: O50335 #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.) Escherichia coli (E. coli) / Gene: trwE / Production host: Escherichia coli (E. coli) / References: UniProt: O50337 |
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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: 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: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.6 |
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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
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) |
-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 |