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Yorodumi- EMDB-13705: cryo electron tomogram of Algoriphagus machipongonensis in bacter... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13705 | |||||||||
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Title | cryo electron tomogram of Algoriphagus machipongonensis in bacterial late stage | |||||||||
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Sample |
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Biological species | Algoriphagus machipongonensis (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Xu J / Ericson C / Feldmueller M / Lien YW / Eisenstein F / Pilhofer M | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: Nat Microbiol / Year: 2022 Title: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Authors: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer / Abstract: Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). ...Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a 'cap adaptor' located at the distal end, a 'plug' exposed to the tube lumen, and a 'cage' formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re-engineering CISs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13705.map.gz | 2 GB | EMDB map data format | |
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Header (meta data) | emd-13705-v30.xml emd-13705.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_13705.png | 165.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13705 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13705 | HTTPS FTP |
-Validation report
Summary document | emd_13705_validation.pdf.gz | 252.7 KB | Display | EMDB validaton report |
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Full document | emd_13705_full_validation.pdf.gz | 252.2 KB | Display | |
Data in XML | emd_13705_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | emd_13705_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13705 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13705 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13705.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.74 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 : marine bacteria Algoriphagus machipongonensis in bacterial late stage
Entire | Name: marine bacteria Algoriphagus machipongonensis in bacterial late stage |
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Components |
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-Supramolecule #1: marine bacteria Algoriphagus machipongonensis in bacterial late stage
Supramolecule | Name: marine bacteria Algoriphagus machipongonensis in bacterial late stage type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: cytodiagnostics / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number real images: 61 / Average electron dose: 2.1 e/Å2 / Details: 61 tilt series with ~130 accumulated dose. |
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 | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61 |
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