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- EMDB-21837: Vibrio alginolyticus Clockwise Locked Rotor -

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Basic information

Entry
Database: EMDB / ID: EMD-21837
TitleVibrio alginolyticus Clockwise Locked Rotor
Map dataclockwise rotor
Sample
  • Organelle or cellular component: Flagellum C-ring in counterclockwise rotation
Biological speciesVibrio alginolyticus (bacteria)
Methodelectron tomography / cryo EM
AuthorsLiu J / Carroll BL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107629 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
CitationJournal: Elife / Year: 2020
Title: The flagellar motor of undergoes major structural remodeling during rotational switching.
Authors: Brittany L Carroll / Tatsuro Nishikino / Wangbiao Guo / Shiwei Zhu / Seiji Kojima / Michio Homma / Jun Liu /
Abstract: The bacterial flagellar motor switches rotational direction between counterclockwise (CCW) and clockwise (CW) to direct the migration of the cell. The cytoplasmic ring (C-ring) of the motor, which is ...The bacterial flagellar motor switches rotational direction between counterclockwise (CCW) and clockwise (CW) to direct the migration of the cell. The cytoplasmic ring (C-ring) of the motor, which is composed of FliG, FliM, and FliN, is known for controlling the rotational sense of the flagellum. However, the mechanism underlying rotational switching remains elusive. Here, we deployed cryo-electron tomography to visualize the C-ring in two rotational biased mutants in . We determined the C-ring molecular architectures, providing novel insights into the mechanism of rotational switching. We report that the C-ring maintained 34-fold symmetry in both rotational senses, and the protein composition remained constant. The two structures show FliG conformational changes elicit a large conformational rearrangement of the rotor complex that coincides with rotational switching of the flagellum. FliM and FliN form a stable spiral-shaped base of the C-ring, likely stabilizing the C-ring during the conformational remodeling.
History
DepositionApr 20, 2020-
Header (metadata) releaseOct 21, 2020-
Map releaseOct 21, 2020-
UpdateOct 21, 2020-
Current statusOct 21, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21837.png

Downloads & links

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Map

FileDownload / File: emd_21837.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationclockwise rotor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 180 pix.
= 612. Å		3.4 Å/pix.
x 180 pix.
= 612. Å		3.4 Å/pix.
x 180 pix.
= 612. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.02
Minimum - Maximum-0.08315589 - 0.17428495
Average (Standard dev.)0.00006571464 (±0.02163675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 612.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.43.43.4
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z612.000612.000612.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0830.1740.000

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Supplemental data

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Sample components

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Entire : Flagellum C-ring in counterclockwise rotation

EntireName: Flagellum C-ring in counterclockwise rotation
Components
  • Organelle or cellular component: Flagellum C-ring in counterclockwise rotation

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Supramolecule #1: Flagellum C-ring in counterclockwise rotation

SupramoleculeName: Flagellum C-ring in counterclockwise rotation / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: Vibrio alginolyicus FliG G214S mutant
Source (natural)Organism: Vibrio alginolyticus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.5 / Details: TMN500 media
VitrificationCryogen name: NITROGEN
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 220

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