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- EMDB-32908: Flagellar motor from wild type H. pylori -

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Basic information

Entry
Database: EMDB / ID: EMD-32908
TitleFlagellar motor from wild type H. pylori
Map datawild type.
Sample
  • Organelle or cellular component: flagellar motor
Biological speciesHelicobacter pylori (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 65.0 Å
AuthorsLu P / Zhang HW / Gao YZ / Jia XD / Liu Z / Wang DP / Au SWA / Zhang QF
Funding support China, Hong Kong, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: mSphere / Year: 2022
Title: Cryo-electron Tomography Reveals the Roles of FliY in Flagellar Motor Assembly.
Authors: Ping Lu / Huawei Zhang / Yuanzhu Gao / Xudong Jia / Zhe Liu / Daping Wang / Shannon Wing Ngor Au / Qinfen Zhang /
Abstract: Helicobacter pylori plays a causative role in gastric diseases. The pathogenicity of H. pylori depends on its ability to colonize the stomach guided by motility. FliY is a unique flagellar motor ...Helicobacter pylori plays a causative role in gastric diseases. The pathogenicity of H. pylori depends on its ability to colonize the stomach guided by motility. FliY is a unique flagellar motor switch component coexisting with the classical FliG, FliM, and FliN switch proteins in some bacteria and has been shown to be essential for flagellation. However, the functional importance of FliY in H. pylori flagellar motor assembly is not well understood. Here, we applied cryo-electron tomography and subtomogram averaging to analyze the structures of flagellar motors from wild-type strain, -null mutant and complementation mutants expressing the N-terminal or C-terminal domain of FliY. Loss of full-length FliY or its C-terminal domain interrupted the formation of an intact C ring and soluble export apparatus, as well as the hook and flagellar filaments. Complementation with FliY C-terminal domain restored all these missing components of flagellar motor. Taken together, these results provide structural insights into the roles of FliY, especially its C-terminal domain in flagellar motor assembly in H. pylori. Helicobacter pylori is the major risk factor related with gastric diseases. Flagellar motor is one of the most important virulence factors in H. pylori. However, the assembly mechanism of H. pylori flagellar motor is not fully understood yet. Previous report mainly described the overall structures of flagellum but had not focused on its specific components. Here, we focus on H. pylori flagellar C-ring protein FliY. We directly visualize the flagellar structures of H. pylori wild-type and FliY N-/C-terminal complementary strains by cryo-electron tomography and subtomogram averaging. Our results show that deletion of FliY or its C-terminal domain causes the loss of C ring, whereas deletion of FliY N-terminal does not affect C-ring assembly and flagellar structures. Our results provide direct evidence that C-ring protein FliY, especially its C-terminal domain, plays an indispensable role in H. pylori motor assembly and flagellar formation. This study will deepen our understanding about H. pylori pathogenesis.
History
DepositionFeb 18, 2022-
SupersessionMar 16, 2022ID: EMD-32012
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBj / 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_32908.png

Downloads & links

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Map

FileDownload / File: emd_32908.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationwild type.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.3 Å/pix.
x 72 pix.
= 1101.29 Å		15.3 Å/pix.
x 72 pix.
= 1101.29 Å		15.3 Å/pix.
x 72 pix.
= 1101.29 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 15.2957 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-1.654485 - 2.8761296
Average (Standard dev.)0.07768416 (±0.9111094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-36-36-36
Dimensions727272
Spacing727272
CellA=B=C: 1101.2904 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z15.29569444444415.29569444444415.295694444444
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z1101.2901101.2901101.290
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-36-36-36
NC/NR/NS727272
D min/max/mean-1.6542.8760.078

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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: Helicobacter pylori (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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 150.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 9.0 µm / Nominal defocus min: 7.0 µm

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Image processing

Final reconstructionApplied symmetry - Point group: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 65.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 59
ExtractionNumber tomograms: 24 / Number images used: 61
Final angle assignmentType: MAXIMUM LIKELIHOOD

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