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Yorodumi- EMDB-4730: Subtomogram average of MAC sheath and inner tube of P. luteoviola... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4730 | |||||||||
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Title | Subtomogram average of MAC sheath and inner tube of P. luteoviolacea Mif1 mutant | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Pseudoalteromonas luteoviolacea (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Eisenstein F / Medeiros J / Pilhofer M | |||||||||
Citation | Journal: Elife / Year: 2019 Title: A contractile injection system stimulates tubeworm metamorphosis by translocating a proteinaceous effector. Authors: Charles F Ericson / Fabian Eisenstein / João M Medeiros / Kyle E Malter / Giselle S Cavalcanti / Robert W Zeller / Dianne K Newman / Martin Pilhofer / Nicholas J Shikuma / Abstract: The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe-animal interaction is ...The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe-animal interaction is critical for the life cycles of diverse marine animals, what types of biochemical cues from bacteria that induce metamorphosis has been a mystery. Metamorphosis of larvae of the tubeworm is induced by arrays of phage tail-like contractile injection systems, which are released by the bacterium . Here we identify the novel effector protein Mif1. By cryo-electron tomography imaging and functional assays, we observe Mif1 as cargo inside the tube lumen of the contractile injection system and show that the gene is required for inducing metamorphosis. Purified Mif1 is sufficient for triggering metamorphosis when electroporated into tubeworm larvae. Our results indicate that the delivery of protein effectors by contractile injection systems may orchestrate microbe-animal interactions in diverse contexts. | |||||||||
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_4730.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-4730-v30.xml emd-4730.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | emd_4730.png | 70.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4730 | HTTPS FTP |
-Validation report
Summary document | emd_4730_validation.pdf.gz | 233.2 KB | Display | EMDB validaton report |
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Full document | emd_4730_full_validation.pdf.gz | 232.3 KB | Display | |
Data in XML | emd_4730_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4730 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4730 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4730.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.29 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 : MAC array
Entire | Name: MAC array |
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Components |
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-Supramolecule #1: MAC array
Supramolecule | Name: MAC array / type: complex / ID: 1 / Parent: 0 / Details: deltaMif1 |
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Source (natural) | Organism: Pseudoalteromonas luteoviolacea (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 13425 |
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Extraction | Number tomograms: 63 / Number images used: 37024 |
Final angle assignment | Type: OTHER |