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Yorodumi- EMDB-9342: Structure of the type VI secretion system TssK-TssF-TssG baseplat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9342 | |||||||||
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Title | Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy - TssK focused mapType VI secretion system | |||||||||
Map data | TssK focused map | |||||||||
Sample |
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Biological species | Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Park YJ / Lacourse KD / Cambillau C / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio F / Mougous JD / Veesler D | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy. Authors: Young-Jun Park / Kaitlyn D Lacourse / Christian Cambillau / Frank DiMaio / Joseph D Mougous / David Veesler / Abstract: Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although ...Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture. | |||||||||
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_9342.map.gz | 5.9 MB | EMDB map data format | |
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Header (meta data) | emd-9342-v30.xml emd-9342.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | emd_9342.png | 213.3 KB | ||
Others | emd_9342_additional.map.gz | 68.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9342 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9342 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9342.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TssK focused map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: TssK focused map - unsharpened
File | emd_9342_additional.map | ||||||||||||
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Annotation | TssK focused map - unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TssK-TssF-TssG T6SS baseplate subcomplex
Entire | Name: TssK-TssF-TssG T6SS baseplate subcomplex |
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Components |
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-Supramolecule #1: TssK-TssF-TssG T6SS baseplate subcomplex
Supramolecule | Name: TssK-TssF-TssG T6SS baseplate subcomplex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.12 mg/mL |
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Buffer | pH: 7.8 |
Grid | Support film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Startup model | Type of model: OTHER Details: An initial model was obtained using cryosparc abinitio. |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36496 |