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- EMDB-1644: Structure of the bacterial flagellar motor from Borrelia -

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Basic information

Entry
Database: EMDB / ID: EMD-1644
TitleStructure of the bacterial flagellar motor from Borrelia
Map dataThis is a 16 fold rotatopnally averaged structure of the bacterial flagellar motor from Borrelia
Sample
  • Sample: Cryo preserved Borrelia spirochetes
  • Organelle or cellular component: Bacterial flagellar motor
KeywordsBacterial flagellar motor / cryo-electron tomography / spirochete
Biological speciesBorrelia burgdorferi group (Lyme Disease Borrelia)
Methodsubtomogram averaging / cryo EM / Resolution: 46.0 Å
AuthorsKudryasheva M / Cyrklaff M / Wallich R / Baumeister W / Frischknecht F
CitationJournal: J Struct Biol / Year: 2010
Title: Distinct in situ structures of the Borrelia flagellar motor.
Authors: Mikhail Kudryashev / Marek Cyrklaff / Reinhard Wallich / Wolfgang Baumeister / Friedrich Frischknecht /
Abstract: Bacteria can be propelled in liquids by flagellar filaments that are attached to and moved by flagellar motors. These motors are rotary nanomachines that use the electrochemical potential from ion ...Bacteria can be propelled in liquids by flagellar filaments that are attached to and moved by flagellar motors. These motors are rotary nanomachines that use the electrochemical potential from ion gradients. The motor can spin in both directions with specific proteins regulating the direction in response to chemotactic stimuli. Here we investigated the structure of flagellar motors of Borrelia spirochetes, the causative agents of Lyme disease in humans. We revealed the structure of the motor complex at 4.6-nm resolution by sub-volume averaging of cryo-electron tomograms and subsequently imposing rotational symmetry. This allowed direct visualisation of individual motor components, the connection between the stator and the peptidoglycan as well as filamentous linkers between the stator and the rod. Two different motor assemblies seem to co-exist at a single bacterial pole. While most motors were completely assembled, a smaller fraction appeared to lack part of the C-ring, which plays a role in protein export and switching the directionality of rotation. Our data suggest a novel mechanism that bacteria may use to control the direction of movement.
History
DepositionAug 19, 2009-
Header (metadata) releaseAug 20, 2009-
Map releaseAug 20, 2009-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

_For_EMDB.tif

Downloads & links

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Map

FileDownload / File: emd_1644.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 16 fold rotatopnally averaged structure of the bacterial flagellar motor from Borrelia
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 128 pix.
= 104.96 Å		0.82 Å/pix.
x 128 pix.
= 104.96 Å		0.82 Å/pix.
x 128 pix.
= 104.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.0.820.820.82
CCP4 map header0.820.820.82
EM Navigator Movie #18.28.28.2
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-4.27202 - 4.28789
Average (Standard dev.)0.0602355 (±0.403399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 104.96 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z104.960104.960104.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-4.2724.2880.060

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Supplemental data

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Sample components

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Entire : Cryo preserved Borrelia spirochetes

EntireName: Cryo preserved Borrelia spirochetes
Components
  • Sample: Cryo preserved Borrelia spirochetes
  • Organelle or cellular component: Bacterial flagellar motor

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Supramolecule #1000: Cryo preserved Borrelia spirochetes

SupramoleculeName: Cryo preserved Borrelia spirochetes / type: sample / ID: 1000
Details: Tomographic subvolume averaging from cryo electron tomography
Number unique components: 25

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Supramolecule #1: Bacterial flagellar motor

SupramoleculeName: Bacterial flagellar motor / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Flagellar motor / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Borrelia burgdorferi group (Lyme Disease Borrelia)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 10.0 µm / Nominal defocus min: 10.0 µm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

CTF correctionDetails: no
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 46.0 Å / Resolution method: OTHER / Software - Name: EM-package, TOM for matlab
Details: The final map is calculated from 107 single motors, 16 fold rotational symmetry applied

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