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- PDB-8rtb: Extended inner membrane complex (IMC) protomer structure (TrwM/Vi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rtb | |||||||||||||||
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Title | Extended inner membrane complex (IMC) protomer structure (TrwM/VirB3-TrwK/VirB4-TrwI/VirB6-TrwG/VirB8-TrwE/VirB10) 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 inner membrane complex IMC IMC-protomer Extended IMC R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB3 VirB4 VirB6 VirB8 VirB10 TrwM TrwK TrwI TrwG TrwE | |||||||||||||||
Function / homology | ![]() protein secretion by the type IV secretion system / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å | |||||||||||||||
![]() | Mace, K. / Waksman, G. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 342.6 KB | Display | ![]() |
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PDB format | ![]() | 264.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 72.4 KB | Display | |
Data in CIF | ![]() | 106.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 19485MC ![]() 8rt4C ![]() 8rt5C ![]() 8rt6C ![]() 8rt7C ![]() 8rt8C ![]() 8rt9C ![]() 8rtaC ![]() 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: 12292.585 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 93769.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: 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.) ![]() ![]() ![]() ![]() #4: Protein | | Mass: 42443.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Protein | | Mass: 35324.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-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: Extended IMC-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: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234578 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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