+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7611 | |||||||||
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Title | Intact Type IV Secretion MachineSecretion | |||||||||
Map data | Intact machine structure | |||||||||
Sample |
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Biological species | Legionella pneumophila (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 33.0 Å | |||||||||
Authors | Liu J / Hu B | |||||||||
Citation | Journal: Nat Microbiol / Year: 2018 Title: A unique cytoplasmic ATPase complex defines the Legionella pneumophila type IV secretion channel. Authors: David Chetrit / Bo Hu / Peter J Christie / Craig R Roy / Jun Liu / Abstract: Type IV secretion systems (T4SSs) are complex machines used by bacteria to deliver protein and DNA complexes into target host cells. Conserved ATPases are essential for T4SS function, but how they ...Type IV secretion systems (T4SSs) are complex machines used by bacteria to deliver protein and DNA complexes into target host cells. Conserved ATPases are essential for T4SS function, but how they coordinate their activities to promote substrate transfer remains poorly understood. Here, we show that the DotB ATPase associates with the Dot-Icm T4SS at the Legionella cell pole through interactions with the DotO ATPase. The structure of the Dot-Icm apparatus was solved in situ by cryo-electron tomography at 3.5 nm resolution and the cytoplasmic complex was solved at 3.0 nm resolution. These structures revealed a cell envelope-spanning channel that connects to the cytoplasmic complex. Further analysis revealed a hexameric assembly of DotO dimers associated with the inner membrane complex, and a DotB hexamer associated with the base of this cytoplasmic complex. The assembly of a DotB-DotO energy complex creates a cytoplasmic channel that directs the translocation of substrates through the T4SS. These data define distinct stages in Dot-Icm machine biogenesis, advance our understanding of channel activation, and identify an envelope-spanning T4SS channel. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7611.map.gz | 10.3 MB | EMDB map data format | |
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Header (meta data) | emd-7611-v30.xml emd-7611.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | emd_7611.png | 155.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7611 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7611 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7611.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Intact machine structure | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Type IV secretion machine
Entire | Name: Type IV secretion machineSecretion |
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Components |
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-Supramolecule #1: Type IV secretion machine
Supramolecule | Name: Type IV secretion machine / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.0 sec. / Average electron dose: 1.5 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 1000 / Number images used: 5000 / Method: manually / Software - Name: IMOD (ver. 4.9.6) |
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CTF correction | Software - Name: IMOD (ver. 4.9.6) |
Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 5000 |