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- EMDB-10057: Plesiomonas shigelloides polar motor -

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Basic information

Entry
Database: EMDB / ID: EMD-10057
TitlePlesiomonas shigelloides polar motor
Map dataSubtomogram average of Plesiomonas shigelloides polar flagellar motor
Sample
  • Complex: Flagellar motor from Plesiomonas shigelloidesFlagellum
Biological speciesPlesiomonas shigelloides ATCC 14029 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsFerreira JF / Beeby M
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P019374/1 United Kingdom
Medical Research Council (United Kingdom)FC001143 United Kingdom
Medical Research Council (United Kingdom)MR/K501281/1 United Kingdom
Cancer Research UKFC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
CitationJournal: 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
DepositionJun 11, 2019-
SupersessionJun 19, 2019ID: EMD-4570
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateJul 24, 2019-
Current statusJul 24, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0369
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0369
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10057.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of Plesiomonas shigelloides polar flagellar motor
Voxel sizeX=Y=Z: 2.713 Å
Density
Contour LevelBy AUTHOR: 0.0369 / Movie #1: 0.0369
Minimum - Maximum-0.19750887 - 0.20718084
Average (Standard dev.)-0.00023747048 (±0.03147648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-30-30-30
Dimensions350350350
Spacing350350350
CellA=B=C: 949.55005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.7132.7132.713
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z949.550949.550949.550
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS350350350
D min/max/mean-0.1980.207-0.000

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Supplemental data

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Sample components

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Entire : Flagellar motor from Plesiomonas shigelloides

EntireName: Flagellar motor from Plesiomonas shigelloidesFlagellum
Components
  • Complex: Flagellar motor from Plesiomonas shigelloidesFlagellum

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Supramolecule #1: Flagellar motor from Plesiomonas shigelloides

SupramoleculeName: Flagellar motor from Plesiomonas shigelloides / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plesiomonas shigelloides ATCC 14029 (bacteria) / Location in cell: cell envelope

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: Cells grown in LB
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 89 / Number images used: 424 / Software - Name: IMOD
CTF correctionSoftware - Name: TOMOCTF
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 389

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