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- EMDB-4569: Flagellar motor relic structure from Plesiomonas shigelloides -

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Basic information

Entry
Database: EMDB / ID: EMD-4569
TitleFlagellar motor relic structure from Plesiomonas shigelloides
Map data
Sample
  • Complex: Flagellar relic structure from Plesiomonas shigelloides
Biological speciesPlesiomonas shigelloides ATCC 14029 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 47.0 Å
AuthorsFerreira JF / Beeby M
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
DepositionJan 28, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateMar 27, 2019-
Current statusMar 27, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.047
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.047
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4569.png

Downloads & links

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Map

FileDownload / File: emd_4569.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.71 Å/pix.
x 250 pix.
= 678.25 Å		2.71 Å/pix.
x 250 pix.
= 678.25 Å		2.71 Å/pix.
x 250 pix.
= 678.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.713 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.047 / Movie #1: 0.047
Minimum - Maximum-0.16810913 - 0.22102694
Average (Standard dev.)0.011475681 (±0.0559221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125-125-125
Dimensions250250250
Spacing250250250
CellA=B=C: 678.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.7132.7132.713
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z678.250678.250678.250
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS250250250
D min/max/mean-0.1680.2210.011

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Supplemental data

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Sample components

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Entire : Flagellar relic structure from Plesiomonas shigelloides

EntireName: Flagellar relic structure from Plesiomonas shigelloides
Components
  • Complex: Flagellar relic structure from Plesiomonas shigelloides

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Supramolecule #1: Flagellar relic structure from Plesiomonas shigelloides

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

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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
GridModel: UltrAuFoil / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

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

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Image processing

Final reconstructionApplied 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
ExtractionNumber tomograms: 89 / Number images used: 124 / Software - Name: IMOD
CTF correctionSoftware - Name: TOMOCTF
Final angle assignmentType: NOT APPLICABLE

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