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- EMDB-21027: Vibrio flagellar motor structure -

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Basic information

Entry
Database: EMDB / ID: EMD-21027
TitleVibrio flagellar motor structure
Map dataVibrio flagellar motor
Sample
  • Organelle or cellular component: Bacterial flagellar motor
Biological speciesVibrio alginolyticus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsZhu S / Nishikino T / Takekawa N / Terashima H / Kojima S / Imada K / Homma M / Liu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107629 United States
CitationJournal: J Bacteriol / Year: 2020
Title: Structure of the Polar Flagellum Reveals a Distinct Outer Membrane Complex and Its Specific Interaction with the Stator.
Authors: Shiwei Zhu / Tatsuro Nishikino / Norihiro Takekawa / Hiroyuki Terashima / Seiji Kojima / Katsumi Imada / Michio Homma / Jun Liu /
Abstract: The bacterial flagellum is a biological nanomachine that rotates to allow bacteria to swim. For flagellar rotation, torque is generated by interactions between a rotor and a stator. The stator, which ...The bacterial flagellum is a biological nanomachine that rotates to allow bacteria to swim. For flagellar rotation, torque is generated by interactions between a rotor and a stator. The stator, which is composed of MotA and MotB subunit proteins in the membrane, is thought to bind to the peptidoglycan (PG) layer, which anchors the stator around the rotor. Detailed information on the stator and its interactions with the rotor remains unclear. Here, we deployed cryo-electron tomography and genetic analysis to characterize structure of the bacterial flagellar motor in , which is best known for its polar sheathed flagellum and high-speed rotation. We determined structure of the motor at unprecedented resolution and revealed the unique protein-protein interactions among -specific features, namely the H ring and T ring. Specifically, the H ring is composed of 26 copies of FlgT and FlgO, and the T ring consists of 26 copies of a MotX-MotY heterodimer. We revealed for the first time a specific interaction between the T ring and the stator PomB subunit, providing direct evidence that the stator unit undergoes a large conformational change from a compact form to an extended form. The T ring facilitates the recruitment of the extended stator units for the high-speed motility in species. The torque of flagellar rotation is generated by interactions between a rotor and a stator; however, detailed structural information is lacking. Here, we utilized cryo-electron tomography and advanced imaging analysis to obtain a high-resolution flagellar basal body structure in , which is a Gram-negative marine bacterium. Our high-resolution motor structure not only revealed detailed protein-protein interactions among unique -specific features, the T ring and H ring, but also provided the first structural evidence that the T ring interacts directly with the periplasmic domain of the stator. Docking atomic structures of key components into the motor map allowed us to visualize the pseudoatomic architecture of the polar sheathed flagellum in spp. and provides novel insight into its assembly and function.
History
DepositionNov 24, 2019-
Header (metadata) releaseDec 25, 2019-
Map releaseNov 25, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21027.png

Downloads & links

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Map

FileDownload / File: emd_21027.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVibrio flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 160 pix.
= 544. Å		3.4 Å/pix.
x 160 pix.
= 544. Å		3.4 Å/pix.
x 160 pix.
= 544. 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 LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-4.7703404 - 6.0104785
Average (Standard dev.)-0.00003040172 (±1.0013539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.43.43.4
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z544.000544.000544.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-4.7706.010-0.000

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Supplemental data

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Sample components

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Entire : Bacterial flagellar motor

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

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Supramolecule #1: Bacterial flagellar motor

SupramoleculeName: Bacterial flagellar motor / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Vibrio alginolyticus (bacteria)

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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: 7
GridModel: Quantifoil R2/4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (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 reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 3000
ExtractionNumber tomograms: 300 / Number images used: 3200
Final 3D classificationNumber classes: 20
Final angle assignmentType: OTHER / Software - Name: PROTOMO

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