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Yorodumi- EMDB-7474: Subtomogram average of the cag type IV secretion system in Helico... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7474 | |||||||||
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Title | Subtomogram average of the cag type IV secretion system in Helicobacter pylori cells (aligning periplasmic parts) | |||||||||
Map data | primary map | |||||||||
Sample |
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Biological species | Helicobacter pylori (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 39.0 Å | |||||||||
Authors | Chang Y-W / Shaffer C / Rettberg LA / Ghosal D / Jensen GJ | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell Rep / Year: 2018 Title: In Vivo Structures of the Helicobacter pylori cag Type IV Secretion System. Authors: Yi-Wei Chang / Carrie L Shaffer / Lee A Rettberg / Debnath Ghosal / Grant J Jensen / Abstract: The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal ...The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal the molecular architecture of the Helicobacter pylori cag T4SS. Although most components are unique to H. pylori, the cag T4SS exhibits remarkable architectural similarity to other T4SSs. Our images revealed that, when H. pylori encounters host cells, the bacterium elaborates membranous tubes perforated by lateral ports. Sub-tomogram averaging of the cag T4SS machinery revealed periplasmic densities associated with the outer membrane, a central stalk, and peripheral wing-like densities. Additionally, we resolved pilus-like rod structures extending from the cag T4SS into the inner membrane, as well as densities within the cytoplasmic apparatus corresponding to a short central barrel surrounded by four longer barrels. Collectively, these studies reveal the structure of a dynamic molecular machine that evolved to function in the human gastric niche. | |||||||||
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_7474.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-7474-v30.xml emd-7474.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_7474.png | 111.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7474 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7474 | HTTPS FTP |
-Validation report
Summary document | emd_7474_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_7474_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_7474_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7474 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7474 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7474.map.gz / Format: CCP4 / Size: 5.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.8 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 : cag type IV secretion system
Entire | Name: cag type IV secretion system |
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Components |
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-Supramolecule #1: cag type IV secretion system
Supramolecule | Name: cag type IV secretion system / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Helicobacter pylori (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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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 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: Tecnai Polara / Image courtesy: FEI Company |