+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3791 | |||||||||
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Title | Cryotomogram of purified Amoebophilus asiaticus cells | |||||||||
Map data | Cryotomogram of purified Amoebophilus asiaticus cells | |||||||||
Sample |
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Biological species | Candidatus Amoebophilus asiaticus 5a2 (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
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. | |||||||||
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_3791.map.gz | 231.3 MB | EMDB map data format | |
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Header (meta data) | emd-3791-v30.xml emd-3791.xml | 7.1 KB 7.1 KB | Display Display | EMDB header |
Images | emd_3791.png | 135.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3791 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3791 | HTTPS FTP |
-Validation report
Summary document | emd_3791_validation.pdf.gz | 155.9 KB | Display | EMDB validaton report |
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Full document | emd_3791_full_validation.pdf.gz | 155 KB | Display | |
Data in XML | emd_3791_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3791 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3791 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3791.map.gz / Format: CCP4 / Size: 384.4 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryotomogram of purified Amoebophilus asiaticus cells | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 19.76 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 : Amoebophilus asiaticus
Entire | Name: Amoebophilus asiaticus |
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Components |
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-Supramolecule #1: Amoebophilus asiaticus
Supramolecule | Name: Amoebophilus asiaticus / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Candidatus Amoebophilus asiaticus 5a2 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Sigma-Aldrich / Diameter: 10 nm |
-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: 1.24 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 121 |
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