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- EMDB-5299: Structural Diversity of Bacterial Flagellar Motors: Helicobacter ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5299
TitleStructural Diversity of Bacterial Flagellar Motors: Helicobacter hepaticus
Map dataFinal map is the C16-symmetrized average calculated from 60 individual sub-tomograms of Helicobacter hepaticus flagellar motors.
Sample
  • Sample: Helicobacter hepaticus flagellar motor
  • Organelle or cellular component: flagellar motorFlagellum
KeywordsHelicobacter hepaticus flagellar motor
Biological speciesHelicobacter hepaticus (bacteria)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 50.0 Å
AuthorsChen S / Beeby M / Murphy GE / Leadbetter JR / Hendrixson DR / Briegel A / Li Z / Shi J / Tocheva EI / Muller A ...Chen S / Beeby M / Murphy GE / Leadbetter JR / Hendrixson DR / Briegel A / Li Z / Shi J / Tocheva EI / Muller A / Dobro MJ / Jensen GJ
CitationJournal: EMBO J / Year: 2011
Title: Structural diversity of bacterial flagellar motors.
Authors: Songye Chen / Morgan Beeby / Gavin E Murphy / Jared R Leadbetter / David R Hendrixson / Ariane Briegel / Zhuo Li / Jian Shi / Elitza I Tocheva / Axel Müller / Megan J Dobro / Grant J Jensen /
Abstract: The bacterial flagellum is one of nature's most amazing and well-studied nanomachines. Its cell-wall-anchored motor uses chemical energy to rotate a microns-long filament and propel the bacterium ...The bacterial flagellum is one of nature's most amazing and well-studied nanomachines. Its cell-wall-anchored motor uses chemical energy to rotate a microns-long filament and propel the bacterium towards nutrients and away from toxins. While much is known about flagellar motors from certain model organisms, their diversity across the bacterial kingdom is less well characterized, allowing the occasional misrepresentation of the motor as an invariant, ideal machine. Here, we present an electron cryotomographical survey of flagellar motor architectures throughout the Bacteria. While a conserved structural core was observed in all 11 bacteria imaged, surprisingly novel and divergent structures as well as different symmetries were observed surrounding the core. Correlating the motor structures with the presence and absence of particular motor genes in each organism suggested the locations of five proteins involved in the export apparatus including FliI, whose position below the C-ring was confirmed by imaging a deletion strain. The combination of conserved and specially-adapted structures seen here sheds light on how this complex protein nanomachine has evolved to meet the needs of different species.
History
DepositionJun 6, 2011-
Header (metadata) releaseSep 22, 2011-
Map releaseSep 22, 2011-
UpdateSep 22, 2011-
Current statusSep 22, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5299_1.png

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Map

FileDownload / File: emd_5299.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map is the C16-symmetrized average calculated from 60 individual sub-tomograms of Helicobacter hepaticus flagellar motors.
Voxel sizeX=Y=Z: 12.64 Å
Density
Contour LevelBy AUTHOR: 25.0 / Movie #1: 25
Minimum - Maximum-73.333399999999997 - 109.811000000000007
Average (Standard dev.)3.0 (±20.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 1137.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z12.6412.6412.64
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z1137.6001137.6001137.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
D min/max/mean-73.333109.8113.000

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Supplemental data

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Sample components

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Entire : Helicobacter hepaticus flagellar motor

EntireName: Helicobacter hepaticus flagellar motor
Components
  • Sample: Helicobacter hepaticus flagellar motor
  • Organelle or cellular component: flagellar motorFlagellum

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Supramolecule #1000: Helicobacter hepaticus flagellar motor

SupramoleculeName: Helicobacter hepaticus flagellar motor / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: flagellar motor

SupramoleculeName: flagellar motor / type: organelle_or_cellular_component / ID: 1 / Name.synonym: flagellar motor / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Helicobacter hepaticus (bacteria) / Strain: ATCC 51449

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging

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Sample preparation

BufferDetails: trypticase soy blood agar in the presence of added gut epithelial host cells
StainingType: NEGATIVE / Details: no staining
GridDetails: EM R2/2 copper/rhodium Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 12.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 34000
Specialist opticsEnergy filter - Name: GATAN GIF / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: FEI Polara / Specimen holder model: GATAN HELIUM / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
TemperatureAverage: 82 K
DateFeb 27, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 200 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Bsoft
Details: Final map is the C16-symmetrized average calculated from 60 individual sub-tomograms.
DetailsAverage number of tilts used in the 3D reconstructions: 120. Average tomographic tilt angle increment: 1.

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