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- EMDB-40219: A subtomogram averaged structure of Helicobacter pylori flagellar... -

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Basic information

Entry
Database: EMDB / ID: EMD-40219
TitleA subtomogram averaged structure of Helicobacter pylori flagellar motor from a flgV deletion mutant.
Map dataA subtomogram averaged structure of H.pylori flagellar motor from dflgV.
Sample
  • Cell: Helicobacter pylori flagellar motor from a flgV deletion mutant
Keywordsflagella / motor / H.pylori / MOTOR PROTEIN
Biological speciesHelicobacter pylori B128 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 31.0 Å
AuthorsLiu J / Tachiyama S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI140444 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI146907 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI087946 United States
CitationJournal: PLoS One / Year: 2023
Title: FlgV forms a flagellar motor ring that is required for optimal motility of Helicobacter pylori.
Authors: Jack M Botting / Shoichi Tachiyama / Katherine H Gibson / Jun Liu / Vincent J Starai / Timothy R Hoover /
Abstract: Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric ...Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. H. pylori has evolved a high-torque-generating flagellar motor that possesses several accessories not found in the archetypical Escherichia coli motor. FlgV was one of the first flagellar accessory proteins identified in Campylobacter jejuni, but its structure and function remain poorly understood. Here, we confirm that deletion of flgV in H. pylori B128 and a highly motile variant of H. pylori G27 (G27M) results in reduced motility in soft agar medium. Comparative analyses of in-situ flagellar motor structures of wild-type, ΔflgV, and a strain expressing FlgV-YFP showed that FlgV forms a ring-like structure closely associated with the junction of two highly conserved flagellar components: the MS and C rings. The results of our studies suggest that the FlgV ring has adapted specifically in Campylobacterota to support the assembly and efficient function of the high-torque-generating motors.
History
DepositionMar 23, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40219.png

Downloads & links

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Map

FileDownload / File: emd_40219.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA subtomogram averaged structure of H.pylori flagellar motor from dflgV.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.59 Å/pix.
x 140 pix.
= 1202.88 Å		8.59 Å/pix.
x 140 pix.
= 1202.88 Å		8.59 Å/pix.
x 140 pix.
= 1202.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.592 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.78844726 - 0.9164692
Average (Standard dev.)-0.000000000070775 (±0.10282089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 1202.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: A half map from the averaged structure of...

Fileemd_40219_half_map_1.map
AnnotationA half map from the averaged structure of H.pylori flagellar motor from dflgV.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map from the averaged structure of...

Fileemd_40219_half_map_2.map
AnnotationA half map from the averaged structure of H.pylori flagellar motor from dflgV.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helicobacter pylori flagellar motor from a flgV deletion mutant

EntireName: Helicobacter pylori flagellar motor from a flgV deletion mutant
Components
  • Cell: Helicobacter pylori flagellar motor from a flgV deletion mutant

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Supramolecule #1: Helicobacter pylori flagellar motor from a flgV deletion mutant

SupramoleculeName: Helicobacter pylori flagellar motor from a flgV deletion mutant
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Helicobacter pylori B128 (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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 1.81 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 9108
ExtractionNumber tomograms: 224 / Number images used: 653
Final angle assignmentType: OTHER

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