[English] 日本語
Yorodumi- EMDB-0566: Subtomogram average of the Legionella pneumophila Dot/Icm type IV... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0566 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Subtomogram average of the Legionella pneumophila Dot/Icm type IV secretion system with DotF fused to a superfolder GFP (aligning the OM-complex) | |||||||||
Map data | Subtomogram average of the Legionella pneumophila Dot/Icm type IV secretion system with DotF fused to a superfolder GFP (aligning the OM-complex). | |||||||||
Sample |
| |||||||||
Biological species | Legionella pneumophila (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 40.0 Å | |||||||||
Authors | Ghosal D / Jeong KC / Chang YW / Vogel JP / Jensen GJ | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Nat Microbiol / Year: 2019 Title: Molecular architecture, polar targeting and biogenesis of the Legionella Dot/Icm T4SS. Authors: Debnath Ghosal / Kwangcheol C Jeong / Yi-Wei Chang / Jacob Gyore / Lin Teng / Adam Gardner / Joseph P Vogel / Grant J Jensen / Abstract: Legionella pneumophila survives and replicates inside host cells by secreting ~300 effectors through the defective in organelle trafficking (Dot)/intracellular multiplication (Icm) type IVB secretion ...Legionella pneumophila survives and replicates inside host cells by secreting ~300 effectors through the defective in organelle trafficking (Dot)/intracellular multiplication (Icm) type IVB secretion system (T4BSS). Here, we used complementary electron cryotomography and immunofluorescence microscopy to investigate the molecular architecture and biogenesis of the Dot/Icm secretion apparatus. Electron cryotomography mapped the location of the core and accessory components of the Legionella core transmembrane subcomplex, revealing a well-ordered central channel that opens into a large, windowed secretion chamber with an unusual 13-fold symmetry. Immunofluorescence microscopy deciphered an early-stage assembly process that begins with the targeting of Dot/Icm components to the bacterial poles. Polar targeting of this T4BSS is mediated by two Dot/Icm proteins, DotU and IcmF, that, interestingly, are homologues of the T6SS membrane complex components TssL and TssM, suggesting that the Dot/Icm T4BSS is a hybrid system. Together, these results revealed that the Dot/Icm complex assembles in an 'axial-to-peripheral' pattern. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0566.map.gz | 3.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0566-v30.xml emd-0566.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_0566.png | 69.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0566 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0566 | HTTPS FTP |
-Validation report
Summary document | emd_0566_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0566_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_0566_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0566 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0566 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_0566.map.gz / Format: CCP4 / Size: 4.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Subtomogram average of the Legionella pneumophila Dot/Icm type IV secretion system with DotF fused to a superfolder GFP (aligning the OM-complex). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Subtomogram average of the Legionella pneumophila Dot/Icm type IV...
Entire | Name: Subtomogram average of the Legionella pneumophila Dot/Icm type IV secretion system with DotF fused to a superfolder GFP (aligning the OM-complex). |
---|---|
Components |
|
-Supramolecule #1: Subtomogram average of the Legionella pneumophila Dot/Icm type IV...
Supramolecule | Name: Subtomogram average of the Legionella pneumophila Dot/Icm type IV secretion system with DotF fused to a superfolder GFP (aligning the OM-complex). type: complex / ID: 1 / Parent: 0 Details: We used electron cryotomography and subtomogram averaging to visualize L. pneumophila Dot/Icm (DotF-GFP fusion) complex directly in intact, frozen-hydrated bacterial cells |
---|---|
Source (natural) | Organism: Legionella pneumophila (bacteria) / Strain: Lp02 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 6.9 |
---|---|
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: 40.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMOD / Number subtomograms used: 254 |
---|---|
Extraction | Number tomograms: 75 / Number images used: 254 / Software - Name: PEET |
Final angle assignment | Type: OTHER |