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- EMDB-10000: Lateral flagellar motor from Plesiomonas shigelloidea -

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Basic information

Entry
Database: EMDB / ID: EMD-10000
TitleLateral flagellar motor from Plesiomonas shigelloidea
Map dataPlesiomonas shigelloides latreal flagellar motor
Sample
  • Complex: Lateral flagellar motor from Plesiomonas shigelloides
Biological speciesPlesiomonas shigelloides (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 120.0 Å
AuthorsFerreira JL / Beeby M
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P019374/1 United Kingdom
Medical Research Council (United Kingdom)MR/K501281/1 United Kingdom
CitationJournal: Front Microbiol / Year: 2021
Title: The "Jack-of-all-Trades" Flagellum From and Was Horizontally Acquired From an Ancestral β-Proteobacterium.
Authors: Josie L Ferreira / Izaak Coleman / Max L Addison / Tobias Zachs / Bonnie L Quigley / Kristin Wuichet / Morgan Beeby /
Abstract: The γ-proteobacteria are a group of diverse bacteria including pathogenic , and species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non- ...The γ-proteobacteria are a group of diverse bacteria including pathogenic , and species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non-chemotactic flagella. Notable exceptions are the enteric Enterobacteriaceae such as and . Many of the well-studied Enterobacteriaceae are gut bacteria that both swim and swarm with the same proton-driven peritrichous flagella. How different flagella evolved in closely related lineages, however, has remained unclear. Here, we describe our phylogenetic finding that Enterobacteriaceae flagella are not native polar or lateral γ-proteobacterial flagella but were horizontally acquired from an ancestral β-proteobacterium. Using electron cryo-tomography and subtomogram averaging, we confirmed that Enterobacteriaceae flagellar motors resemble contemporary β-proteobacterial motors and are distinct to the polar and lateral motors of other γ-proteobacteria. Structural comparisons support a model in which γ-proteobacterial motors have specialized, suggesting that acquisition of a β-proteobacterial flagellum may have been beneficial as a general-purpose motor suitable for adjusting to diverse conditions. This acquisition may have played a role in the development of the enteric lifestyle.
History
DepositionMay 23, 2019-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10000.png

Downloads & links

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Map

FileDownload / File: emd_10000.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlesiomonas shigelloides latreal flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.28 Å/pix.
x 100 pix.
= 828. Å		8.28 Å/pix.
x 100 pix.
= 828. Å		8.28 Å/pix.
x 100 pix.
= 828. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.11
Minimum - Maximum-0.55448806 - 0.667116
Average (Standard dev.)0.016991854 (±0.13127448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-10-10
Dimensions100100100
Spacing100100100
CellA=B=C: 828.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.288.288.28
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z828.000828.000828.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-10-20-10
NC/NR/NS100100100
D min/max/mean-0.5540.6670.017

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Supplemental data

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Sample components

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Entire : Lateral flagellar motor from Plesiomonas shigelloides

EntireName: Lateral flagellar motor from Plesiomonas shigelloides
Components
  • Complex: Lateral flagellar motor from Plesiomonas shigelloides

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Supramolecule #1: Lateral flagellar motor from Plesiomonas shigelloides

SupramoleculeName: Lateral flagellar motor from Plesiomonas shigelloides / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plesiomonas shigelloides (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7 / Details: LB
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsCells grown to OD600 0.6 in LB, lysed with penicillin G

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 6 / Average exposure time: 0.8 sec. / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C100 (100 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 120.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 317
ExtractionNumber tomograms: 200 / Number images used: 220
Final angle assignmentType: OTHER

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