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- EMDB-6088: Electron cryo-tomography of flagellar motor from Borrelia burgdorferi -

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Basic information

Entry
Database: EMDB / ID: EMD-6088
TitleElectron cryo-tomography of flagellar motor from Borrelia burgdorferi
Map dataReconstruction of mutant Borrelia burgdorferi flagellar motor
Sample
  • Sample: Flagellar motor mutant from Borrelia burgdorferi (FlhA mutant)
  • Organelle or cellular component: flagellar motor
KeywordsFlhA / type III secretion / flagellar motor / Borrelia burgdorferi / ATPase
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Methodsubtomogram averaging / cryo EM / Resolution: 38.0 Å
AuthorsTu JG / Zhao XW / Manne A / Lees K / Yerke A / Zhang K / Li CH / Norris SJ / Motaleb MA / Liu J
CitationJournal: To Be Published
Title: Molecular architecture and secretion mechanism of the flagellar type III secretion machine in Borrelia burgdorferi
Authors: Tu JG / Zhao XW / Manne A / Lees K / Yerke A / Zhang K / Li CH / Norris SJ / Motaleb MA / Liu J
History
DepositionSep 13, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseSep 30, 2015-
UpdateSep 30, 2015-
Current statusSep 30, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.31
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6088.jpg

Downloads & links

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Map

FileDownload / File: emd_6088.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mutant Borrelia burgdorferi flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.6 Å/pix.
x 256 pix.
= 1433.6 Å		5.6 Å/pix.
x 256 pix.
= 1433.6 Å		5.6 Å/pix.
x 256 pix.
= 1433.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.31 / Movie #1: 1.31
Minimum - Maximum-18.638338090000001 - 19.951128010000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 1433.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.65.65.6
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1433.6001433.6001433.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-18.63819.9510.000

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Supplemental data

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Sample components

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Entire : Flagellar motor mutant from Borrelia burgdorferi (FlhA mutant)

EntireName: Flagellar motor mutant from Borrelia burgdorferi (FlhA mutant)
Components
  • Sample: Flagellar motor mutant from Borrelia burgdorferi (FlhA mutant)
  • Organelle or cellular component: flagellar motor

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Supramolecule #1000: Flagellar motor mutant from Borrelia burgdorferi (FlhA mutant)

SupramoleculeName: Flagellar motor mutant from Borrelia burgdorferi (FlhA mutant)
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 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Borrelia burgdorferi (Lyme disease spirochete)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
DateMay 4, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 1.5 µm / Number real images: 87
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: OTHER / Software - Name: IMOD, Protomo / Number subtomograms used: 2007

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