+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8544 | |||||||||
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Title | Salmonella Type III secretion injectisome | |||||||||
Map data | Salmonella injectisome | |||||||||
Sample |
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Biological species | Salmonella (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 17.0 Å | |||||||||
Authors | Hu B / Liu J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2017 Title: In Situ Molecular Architecture of the Salmonella Type III Secretion Machine. Authors: Bo Hu / Maria Lara-Tejero / Qingke Kong / Jorge E Galán / Jun Liu / Abstract: Type III protein secretion systems have specifically evolved to deliver bacterially encoded proteins into target eukaryotic cells. The core elements of this multi-protein machine are the envelope- ...Type III protein secretion systems have specifically evolved to deliver bacterially encoded proteins into target eukaryotic cells. The core elements of this multi-protein machine are the envelope-associated needle complex, the inner membrane export apparatus, and a large cytoplasmic sorting platform. Here, we report a high-resolution in situ structure of the Salmonella Typhimurium type III secretion machine obtained by high-throughput cryo-electron tomography and sub-tomogram averaging. Through molecular modeling and comparative analysis of machines assembled with protein-tagged components or from different deletion mutants, we determined the molecular architecture of the secretion machine in situ and localized its structural components. We also show that docking of the sorting platform results in significant conformational changes in the needle complex to provide the symmetry adaptation required for the assembly of the entire secretion machine. These studies provide major insight into the structure and assembly of a broadly distributed protein secretion machine. | |||||||||
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_8544.map.gz | 81.1 MB | EMDB map data format | |
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Header (meta data) | emd-8544-v30.xml emd-8544.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_8544.png | 51.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8544 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8544 | HTTPS FTP |
-Validation report
Summary document | emd_8544_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_8544_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_8544_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8544 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8544 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8544.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Salmonella injectisome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.6 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 : Injectisome
Entire | Name: Injectisome |
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Components |
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-Supramolecule #1: Injectisome
Supramolecule | Name: Injectisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella (bacteria) |
Molecular weight | Theoretical: 10 MDa |
-Macromolecule #1: Injectisome
Macromolecule | Name: Injectisome / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Sequence | String: N |
-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 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DARK FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 5274 |
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Extraction | Number tomograms: 1470 / Number images used: 5274 / Software - Name: IMOD |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: i3 |