+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4569 | |||||||||
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Title | Flagellar motor relic structure from Plesiomonas shigelloides | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Plesiomonas shigelloides ATCC 14029 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 47.0 Å | |||||||||
Authors | Ferreira JF / Beeby M | |||||||||
Citation | Journal: PLoS Biol / Year: 2019 Title: γ-proteobacteria eject their polar flagella under nutrient depletion, retaining flagellar motor relic structures. Authors: Josie L Ferreira / Forson Z Gao / Florian M Rossmann / Andrea Nans / Susanne Brenzinger / Rohola Hosseini / Amanda Wilson / Ariane Briegel / Kai M Thormann / Peter B Rosenthal / Morgan Beeby / Abstract: Bacteria switch only intermittently to motile planktonic lifestyles under favorable conditions. Under chronic nutrient deprivation, however, bacteria orchestrate a switch to stationary phase, ...Bacteria switch only intermittently to motile planktonic lifestyles under favorable conditions. Under chronic nutrient deprivation, however, bacteria orchestrate a switch to stationary phase, conserving energy by altering metabolism and stopping motility. About two-thirds of bacteria use flagella to swim, but how bacteria deactivate this large molecular machine remains unclear. Here, we describe the previously unreported ejection of polar motors by γ-proteobacteria. We show that these bacteria eject their flagella at the base of the flagellar hook when nutrients are depleted, leaving a relic of a former flagellar motor in the outer membrane. Subtomogram averages of the full motor and relic reveal that this is an active process, as a plug protein appears in the relic, likely to prevent leakage across their outer membrane; furthermore, we show that ejection is triggered only under nutritional depletion and is independent of the filament as a possible mechanosensor. We show that filament ejection is a widespread phenomenon demonstrated by the appearance of relic structures in diverse γ-proteobacteria including Plesiomonas shigelloides, Vibrio cholerae, Vibrio fischeri, Shewanella putrefaciens, and Pseudomonas aeruginosa. While the molecular details remain to be determined, our results demonstrate a novel mechanism for bacteria to halt costly motility when nutrients become scarce. | |||||||||
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_4569.map.gz | 53.7 MB | EMDB map data format | |
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Header (meta data) | emd-4569-v30.xml emd-4569.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | emd_4569.png | 60.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4569 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4569 | HTTPS FTP |
-Validation report
Summary document | emd_4569_validation.pdf.gz | 283.3 KB | Display | EMDB validaton report |
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Full document | emd_4569_full_validation.pdf.gz | 282.4 KB | Display | |
Data in XML | emd_4569_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4569 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4569 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4569.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.713 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 : Flagellar relic structure from Plesiomonas shigelloides
Entire | Name: Flagellar relic structure from Plesiomonas shigelloides |
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Components |
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-Supramolecule #1: Flagellar relic structure from Plesiomonas shigelloides
Supramolecule | Name: Flagellar relic structure from Plesiomonas shigelloides type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Plesiomonas shigelloides ATCC 14029 (bacteria) / Location in cell: Outer membrane |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: Cells grown in LB |
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Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / 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) / Average exposure time: 2.0 sec. / 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: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 124 |
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Extraction | Number tomograms: 89 / Number images used: 124 / Software - Name: IMOD |
CTF correction | Software - Name: TOMOCTF |
Final angle assignment | Type: NOT APPLICABLE |