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- EMDB-3161: Campylobacter jejuni pflB deletion bacterial flagellar motor -

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Basic information

Entry
Database: EMDB / ID: EMD-3161
TitleCampylobacter jejuni pflB deletion bacterial flagellar motor
Map dataCampylobacter jejuni pflB deletion bacterial flagellar motor
Sample
  • Sample: Campylobacter jejuni pflB deletion bacterial flagellar motor
  • Organelle or cellular component: Bacterial flagellar motor
Keywordsbacterial flagellar motor / flagellar diversity / electron cryo-tomography / Campylobacter jejuni / Vibrio fischeri / Salmonella enterica
Biological speciesCampylobacter jejuni (Campylobacter)
Methodsubtomogram averaging / cryo EM / Resolution: 61.9 Å
AuthorsBeeby M
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold.
Authors: Morgan Beeby / Deborah A Ribardo / Caitlin A Brennan / Edward G Ruby / Grant J Jensen / David R Hendrixson /
Abstract: Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic ...Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes.
History
DepositionSep 18, 2015-
Header (metadata) releaseSep 30, 2015-
Map releaseMar 23, 2016-
UpdateMar 23, 2016-
Current statusMar 23, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0772
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0772
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3161_Cam...

Downloads & links

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Map

FileDownload / File: emd_3161.map.gz / Format: CCP4 / Size: 24 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCampylobacter jejuni pflB deletion bacterial flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.12 Å/pix.
x 186 pix.
= 1510.692 Å		8.12 Å/pix.
x 186 pix.
= 1510.692 Å		8.12 Å/pix.
x 186 pix.
= 1510.692 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0772 / Movie #1: 0.0772
Minimum - Maximum-0.6948694 - 0.57766479
Average (Standard dev.)0.00138426 (±0.08889733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-93-93-93
Dimensions186186186
Spacing186186186
CellA=B=C: 1510.6919 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.1228.1228.122
M x/y/z186186186
origin x/y/z0.0000.0000.000
length x/y/z1510.6921510.6921510.692
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-93-93-93
NC/NR/NS186186186
D min/max/mean-0.6950.5780.001

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Supplemental data

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Sample components

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Entire : Campylobacter jejuni pflB deletion bacterial flagellar motor

EntireName: Campylobacter jejuni pflB deletion bacterial flagellar motor
Components
  • Sample: Campylobacter jejuni pflB deletion bacterial flagellar motor
  • Organelle or cellular component: Bacterial flagellar motor

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Supramolecule #1000: Campylobacter jejuni pflB deletion bacterial flagellar motor

SupramoleculeName: Campylobacter jejuni pflB deletion bacterial flagellar motor
type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 1
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa

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Supramolecule #1: Bacterial flagellar motor

SupramoleculeName: Bacterial flagellar motor / type: organelle_or_cellular_component / ID: 1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Strain: 81-176 / Location in cell: Cell wall

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Variable

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 1, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 120 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -4.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Nitrogen cooled Gatan 914 / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsAveraged using PEET
Final reconstructionApplied symmetry - Point group: C17 (17 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 61.9 Å / Resolution method: OTHER / Software - Name: IMOD / Number subtomograms used: 156
CTF correctionDetails: Low-pass filter
FSC plot (resolution estimation)

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