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Yorodumi- EMDB-4695: Volta phase plate in situ tomogram of an enteroaggregative Escher... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4695 | |||||||||
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Title | Volta phase plate in situ tomogram of an enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus. | |||||||||
Map data | Volta phase plate in situ tomogram of an enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus. | |||||||||
Sample |
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Biological species | Escherichia coli 042 (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Szwedziak P / Pilhofer M | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Bidirectional contraction of a type six secretion system. Authors: Piotr Szwedziak / Martin Pilhofer / Abstract: Contractile injection systems (CISs) mediate cell-cell interactions by a phage tail-like apparatus. Their conserved mechanism relies on the anchoring of the proximal end of a sheath-tube module to a ...Contractile injection systems (CISs) mediate cell-cell interactions by a phage tail-like apparatus. Their conserved mechanism relies on the anchoring of the proximal end of a sheath-tube module to a membrane, followed by contraction of the sheath towards the attachment site and ejection of the inner tube. Here we reveal a major variation of the CIS mechanism in the type six secretion system (T6SS) of enteroaggregative Escherichia coli (EAEC). We show that both ends of the sheath-tube module are attached to opposite sides of the cell, enabling the structure to contract in two opposite directions. The protein TssA1 mediates the interaction of the distal end with the cell envelope, the termination of tail elongation, and non-canonical contraction towards the distal end. We provide a framework for the molecular processes at the T6SS distal end. Further research will address whether bidirectional contraction allows for bidirectional effector secretion. The unrecognized concept of non-canonical contractions could be relevant to biofilms of the human intestine. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4695.map.gz | 429.6 MB | EMDB map data format | |
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Header (meta data) | emd-4695-v30.xml emd-4695.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_4695.png | 167 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4695 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4695 | HTTPS FTP |
-Validation report
Summary document | emd_4695_validation.pdf.gz | 149.5 KB | Display | EMDB validaton report |
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Full document | emd_4695_full_validation.pdf.gz | 148.6 KB | Display | |
Data in XML | emd_4695_validation.xml.gz | 3.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4695 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4695 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4695.map.gz / Format: CCP4 / Size: 594.7 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Volta phase plate in situ tomogram of an enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 21.67 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 : Enteroaggregative Escherichia coli cell displaying a type six sec...
Entire | Name: Enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus. |
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Components |
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-Supramolecule #1: Enteroaggregative Escherichia coli cell displaying a type six sec...
Supramolecule | Name: Enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus. type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli 042 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Cytodiagnostics / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 121 |
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