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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2567 | |||||||||
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Title | Structure of a bacterial Type IV secretion system | |||||||||
![]() | Structure of a bacterial Type IV secretion system | |||||||||
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![]() | Type IV secretion system / R388 conjugative plasmid / Escherichia coli / negative stain electron microscopy | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
![]() | Low HH / Gubellini F / Rivera-Calzada A / Braun N / Connery S / Dujeancourt A / Lu F / Redzej A / Fronzes R / Orlova EV / Waksman G | |||||||||
![]() | ![]() Title: Structure of a type IV secretion system. Authors: Harry H Low / Francesca Gubellini / Angel Rivera-Calzada / Nathalie Braun / Sarah Connery / Annick Dujeancourt / Fang Lu / Adam Redzej / Rémi Fronzes / Elena V Orlova / Gabriel Waksman / ![]() ![]() Abstract: Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification ...Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification of human cells. Given the complex choreography of the substrate through the secretion apparatus, the molecular mechanism of the type IV secretion system has proved difficult to dissect in the absence of structural data for the entire machinery. Here we use electron microscopy to reconstruct the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid. We show that eight proteins assemble in an intricate stoichiometric relationship to form an approximately 3 megadalton nanomachine that spans the entire cell envelope. The structure comprises an outer membrane-associated core complex connected by a central stalk to a substantial inner membrane complex that is dominated by a battery of 12 VirB4 ATPase subunits organized as side-by-side hexameric barrels. Our results show a secretion system with markedly different architecture, and consequently mechanism, to other known bacterial secretion systems. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 802.3 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.9 KB 8.9 KB | Display Display | ![]() |
Images | ![]() | 636.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 196.1 KB | Display | ![]() |
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Full document | ![]() | 195.3 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Structure of a bacterial Type IV secretion system | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Structure of a bacterial Type IV secretion system from Escherichi...
Entire | Name: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmid |
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Components |
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-Supramolecule #1000: Structure of a bacterial Type IV secretion system from Escherichi...
Supramolecule | Name: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmid type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 3 MDa / Theoretical: 3.4 MDa Method: Calculation based on stoichiometry determination of individual components within the complex |
-Macromolecule #1: Type IV secretion system from R388 conjugative plasmid
Macromolecule | Name: Type IV secretion system from R388 conjugative plasmid type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 3 MDa / Theoretical: 3.4 MDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 8 Details: 50 mM Tris-HCl pH 8.0, 200 mM NaCl, 0.06 % w/v DM-NPG, 0.1 % w/v digitonin, 1 mM DTT and 1mM EDTA |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds. |
Grid | Details: Glow-discharged carbon-coated copper grids (Agar Scientific) |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jun 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 693 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 45500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45500 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Number images used: 3200 |
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Final two d classification | Number classes: 803 |