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- EMDB-0534: Asymmetric reconstruction of the in situ flagellar motor structur... -

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Basic information

Entry
Database: EMDB / ID: EMD-0534
TitleAsymmetric reconstruction of the in situ flagellar motor structure in Borrelia burgdorferi
Map datasubtomogram average of the motor structure in wild type Borrelia burgdorferi
Sample
  • Organelle or cellular component: flagellar motor
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsLiu J / Chang YJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01AI087946 United States
National Institutes of Health/National Institute of General Medical SciencesR01GM107629 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01AI132818 United States
CitationJournal: Elife / Year: 2019
Title: Structural insights into flagellar stator-rotor interactions.
Authors: Yunjie Chang / Ki Hwan Moon / Xiaowei Zhao / Steven J Norris / Md A Motaleb / Jun Liu /
Abstract: The bacterial flagellar motor is a molecular machine that can rotate the flagellar filament at high speed. The rotation is generated by the stator-rotor interaction, coupled with an ion flux through ...The bacterial flagellar motor is a molecular machine that can rotate the flagellar filament at high speed. The rotation is generated by the stator-rotor interaction, coupled with an ion flux through the torque-generating stator. Here we employed cryo-electron tomography to visualize the intact flagellar motor in the Lyme disease spirochete, . By analyzing the motor structures of wild-type and stator-deletion mutants, we not only localized the stator complex in situ, but also revealed the stator-rotor interaction at an unprecedented detail. Importantly, the stator-rotor interaction induces a conformational change in the flagella C-ring. Given our observation that a non-motile mutant, in which proton flux is blocked, cannot generate the similar conformational change, we propose that the proton-driven torque is responsible for the conformational change required for flagellar rotation.
History
DepositionFeb 8, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseSep 25, 2019-
UpdateSep 25, 2019-
Current statusSep 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0534.png

Downloads & links

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Map

FileDownload / File: emd_0534.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of the motor structure in wild type Borrelia burgdorferi
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5 Å/pix.
x 200 pix.
= 1000. Å		5 Å/pix.
x 200 pix.
= 1000. Å		5 Å/pix.
x 200 pix.
= 1000. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.05
Minimum - Maximum-0.72353953 - 0.6946537
Average (Standard dev.)-0.0004554716 (±0.06947395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 1000.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z555
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1000.0001000.0001000.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.7240.695-0.000

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Supplemental data

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Sample components

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Entire : flagellar motor

EntireName: flagellar motor
Components
  • Organelle or cellular component: flagellar motor

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Supramolecule #1: flagellar motor

SupramoleculeName: flagellar motor / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Borreliella 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

BufferpH: 6.8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 5919
ExtractionNumber tomograms: 2500 / Number images used: 14678
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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