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- EMDB-6094: Electron cryo-tomography of flagellar motor from Borrelia burgdor... -

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Basic information

Entry
Database: EMDB / ID: EMD-6094
TitleElectron cryo-tomography of flagellar motor from Borrelia burgdorferi (FlhA, FlhB, FliP, FliQ and FliR deletion mutant)
Map dataReconstruction of mutant of Borrelia burgdorferi flagellar motor (FlhA, FlhB, FliP, FliQ, FliR mutant)
Sample
  • Sample: Flagellar motor mutant from Borrelia burgdorferi (FlhA, FlhB, FliP, FliQ and FliR mutant)
  • Organelle or cellular component: flagellar motor
KeywordsFlhA / FlhB / FliP / FliQ / FliR / type III secretion / flagellar motor / Borrelia burgdorferi / ATPase
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Methodsubtomogram averaging / cryo EM / Resolution: 63.0 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 14, 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: 3.57
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.57
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6094.jpg

Downloads & links

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Map

FileDownload / File: emd_6094.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mutant of Borrelia burgdorferi flagellar motor (FlhA, FlhB, FliP, FliQ, FliR mutant)
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: 3.57 / Movie #1: 3.57
Minimum - Maximum-9.32736588 - 11.415907860000001
Average (Standard dev.)0.0 (±0.99999994)
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-9.32711.416-0.000

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Supplemental data

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Sample components

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Entire : Flagellar motor mutant from Borrelia burgdorferi (FlhA, FlhB, Fli...

EntireName: Flagellar motor mutant from Borrelia burgdorferi (FlhA, FlhB, FliP, FliQ and FliR mutant)
Components
  • Sample: Flagellar motor mutant from Borrelia burgdorferi (FlhA, FlhB, FliP, FliQ and FliR mutant)
  • Organelle or cellular component: flagellar motor

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Supramolecule #1000: Flagellar motor mutant from Borrelia burgdorferi (FlhA, FlhB, Fli...

SupramoleculeName: Flagellar motor mutant from Borrelia burgdorferi (FlhA, FlhB, FliP, FliQ and FliR 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
DateJul 15, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
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: 63.0 Å / Resolution method: OTHER / Software - Name: IMOD, Protomo / Number subtomograms used: 54

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