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Yorodumi- EMDB-11750: sub-tomogram averaging of an extracellular contractile injection ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11750 | ||||||||||||
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Title | sub-tomogram averaging of an extracellular contractile injection system mutant (effector deficient mutant) in marine bacterium Algoriphagus machipongonensis | ||||||||||||
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Sample |
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Function / homology | Function and homology information | ||||||||||||
Biological species | Algoriphagus machipongonensis (bacteria) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 32.0 Å | ||||||||||||
Authors | Xu J / Ericson C / Feldmueller M / Lien YW / Pilhofer M | ||||||||||||
Funding support | Switzerland, 3 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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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11750.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-11750-v30.xml emd-11750.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_11750.png | 12.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11750 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11750 | HTTPS FTP |
-Validation report
Summary document | emd_11750_validation.pdf.gz | 280.6 KB | Display | EMDB validaton report |
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Full document | emd_11750_full_validation.pdf.gz | 280.2 KB | Display | |
Data in XML | emd_11750_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_11750_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11750 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11750 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11750.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 11 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 : The overall structure of an extracellular contractile injection s...
Entire | Name: The overall structure of an extracellular contractile injection system mutant in marine bacterium Algoriphagus machipongonensis (effector deficient mutant). |
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Components |
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-Supramolecule #1: The overall structure of an extracellular contractile injection s...
Supramolecule | Name: The overall structure of an extracellular contractile injection system mutant in marine bacterium Algoriphagus machipongonensis (effector deficient mutant). type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 130.0 e/Å2 |
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 | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 404 |
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Extraction | Number tomograms: 46 / Number images used: 404 |
Final angle assignment | Type: PROJECTION MATCHING |