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Yorodumi- EMDB-8567: In vivo structure of the Legionella pneumophila Dot/Icm type IV s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8567 | |||||||||
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Title | In vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system (aligning the inner membrane complex) | |||||||||
Map data | In vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system (aligning the inner membrane complex) | |||||||||
Sample |
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Biological species | Legionella pneumophila (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 30.0 Å | |||||||||
Authors | Ghosal D / Chang YW / Jensen GJ | |||||||||
Citation | Journal: EMBO Rep / Year: 2017 Title: structure of the Dot/Icm type IV secretion system by electron cryotomography. Authors: Debnath Ghosal / Yi-Wei Chang / Kwangcheol C Jeong / Joseph P Vogel / Grant J Jensen / Abstract: Type IV secretion systems (T4SSs) are large macromolecular machines that translocate protein and DNA and are involved in the pathogenesis of multiple human diseases. Here, using electron ...Type IV secretion systems (T4SSs) are large macromolecular machines that translocate protein and DNA and are involved in the pathogenesis of multiple human diseases. Here, using electron cryotomography (ECT), we report the structure of the Dot/Icm type IVB secretion system (T4BSS) utilized by the human pathogen This is the first structure of a type IVB secretion system, and also the first structure of any T4SS While the Dot/Icm system shares almost no sequence similarity with type IVA secretion systems (T4ASSs), its overall structure is seen here to be remarkably similar to previously reported T4ASS structures (those encoded by the R388 plasmid in and the cag pathogenicity island in ). This structural similarity suggests shared aspects of mechanism. However, compared to the negative-stain reconstruction of the purified T4ASS from the R388 plasmid, the Dot/Icm system is approximately twice as long and wide and exhibits several additional large densities, reflecting type-specific elaborations and potentially better structural preservation . | |||||||||
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_8567.map.gz | 3.9 MB | EMDB map data format | |
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Header (meta data) | emd-8567-v30.xml emd-8567.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_8567.png | 67.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8567 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8567 | HTTPS FTP |
-Validation report
Summary document | emd_8567_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_8567_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_8567_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8567 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8567 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8567.map.gz / Format: CCP4 / Size: 4.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | In vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system (aligning the inner membrane complex) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.4 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 : Legionella pneumophila Dot/Icm type IVB secretion system
Entire | Name: Legionella pneumophila Dot/Icm type IVB secretion system |
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Components |
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-Supramolecule #1: Legionella pneumophila Dot/Icm type IVB secretion system
Supramolecule | Name: Legionella pneumophila Dot/Icm type IVB secretion system type: complex / ID: 1 / Parent: 0 Details: We used electron cryotomography and subtomogram averaging to visualize L. pneumophila Dot/Icm machines directly in intact, frozen-hydrated bacteria cells. |
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Source (natural) | Organism: Legionella pneumophila (bacteria) / Strain: Lp02 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 6.9 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: IMOD, TOMO3D / Details: RESMAP / Number subtomograms used: 386 |
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Extraction | Number tomograms: 87 / Number images used: 386 / Software - Name: PEET |
Final angle assignment | Type: OTHER |