|Entry||Database: EMDB / ID: 3795|
|Title||Subtomogram average of extended contractile injection systems|
|Map data||Subtomogram average of extended contractile injection systems|
|Sample||Extended contractile injection system:|
|Source||Candidatus Amoebophilus asiaticus 5a2 (bacteria)|
|Method||subtomogram averaging / cryo EM / 40 Å resolution|
|Authors||Boeck D / Medeiros JM|
|Citation||Journal: Science / Year: 2017|
Title: In situ architecture, function, and evolution of a contractile injection system.
Authors: Désirée Böck / João M Medeiros / Han-Fei Tsao / Thomas Penz / Gregor L Weiss / Karin Aistleitner / Matthias Horn / Martin Pilhofer
Abstract: Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by ...Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by intracellular localization and attachment to the cytoplasmic membrane. Here we used cryo-focused ion beam milling, electron cryotomography, and functional assays to study a T6SS in The in situ architecture revealed three modules, including a contractile sheath-tube, a baseplate, and an anchor. All modules showed conformational changes upon firing. Lateral baseplate interactions coordinated T6SSs in hexagonal arrays. The system mediated interactions with host membranes and may participate in phagosome escape. Evolutionary sequence analyses predicted that T6SSs are more widespread than previously thought. Our insights form the basis for understanding T6SS key concepts and exploring T6SS diversity.
|Date||Deposition: Jul 10, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Aug 23, 2017 / Last update: Aug 30, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3795.map.gz (map file in CCP4 format, 961 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 8.1 Å|
CCP4 map header:
-Entire Extended contractile injection system
|Entire||Name: Extended contractile injection system / Number of components: 1|
-Component #1: protein, Extended contractile injection system
|Protein||Name: Extended contractile injection system / Recombinant expression: No|
|Source||Species: Candidatus Amoebophilus asiaticus 5a2 (bacteria)|
|Specimen||Specimen state: cell / Method: cryo EM|
|Sample solution||pH: 7|
|Vitrification||Cryogen name: OTHER|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.24 e/Å2 / Illumination mode: OTHER|
|Lens||Imaging mode: OTHER|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic) / Number of subtomograms: 243|
|3D reconstruction||Resolution: 4 Å / Resolution method: FSC 0.5 CUT-OFF|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi