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- EMDB-3813: Tomogram of the salmonella enterica wild-type bacterial flagellar... -

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Basic information

Entry
Database: EMDB / ID: EMD-3813
TitleTomogram of the salmonella enterica wild-type bacterial flagellar motor
Map data
Sample
  • Organelle or cellular component: Salmonella enterica Flagellar motor
Biological speciesSalmonella (bacteria)
Methodelectron tomography / cryo EM
AuthorsBeeby M / Ribardo DA / Brennan CA / Ruby EG / Jensen GJ / Hendrixson DR
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
DepositionJul 14, 2017-
Header (metadata) releaseJul 26, 2017-
Map releaseJul 26, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3813.png

Downloads & links

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Map

FileDownload / File: emd_3813.map.gz / Format: CCP4 / Size: 400 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 8.122 Å
Density
Minimum - Maximum-128. - 127.
Average (Standard dev.)56.306488000000002 (±8.228934000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-400
Dimensions10241024400
Spacing10241024400
CellA: 8316.928 Å / B: 8316.928 Å / C: 3248.7998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z8.1228.1228.122
M x/y/z10241024400
origin x/y/z0.0000.0000.000
length x/y/z8316.9288316.9283248.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-400
NC/NR/NS10241024400
D min/max/mean-128.000127.00056.306

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Supplemental data

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Sample components

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Entire : Salmonella enterica Flagellar motor

EntireName: Salmonella enterica Flagellar motor
Components
  • Organelle or cellular component: Salmonella enterica Flagellar motor

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Supramolecule #1: Salmonella enterica Flagellar motor

SupramoleculeName: Salmonella enterica Flagellar motor / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Salmonella (bacteria) / Strain: TH16943 / Location in cell: Cell wall

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
Details: PH is not know. PH of 7 was added because PH is a mandatory item.
GridModel: Quantifoil R2/2 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Details: Quantifoil R2/2 grids (200-mesh) (Quantifoil Micro Tools GmbH) were glow-discharged for 60 s at 10 mA.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III
DetailsSalmonella strain TH16943 (ParaftsZ) was grown aerobically overnight in LB broth from freezer stocks at 37C. After overnight culture, 50 uL of 5% (wt/vol) L-arabinose were added to 5 mL fresh LB broth for each culture, and cultures were incubated for an additional 5 h. To enrich for minicells, 3 mL this culture were spun at 6,000 x g for 5 min, and the supernatant was recovered. The supernatant was spin-concentrated by centrifugation at 18,000 x g for 5 min, and the resultant pellet was resuspended in 50 uL LB broth and was immediately plunge-frozen.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma-Aldrich / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 1024 pixel / Digitization - Dimensions - Height: 1024 pixel / Number grids imaged: 1 / Average electron dose: 0.6 e/Å2

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Image processing

CTF correctionSoftware - Name: TOMOCTF
Software - details: High-defocus datasets were contrast transfer function (CTF)-corrected
Final reconstructionResolution method: OTHER / Software: (Name: IMOD, RAPTOR, Leginon) / Number images used: 201

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