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- EMDB-48132: In situ structure of the Helicobacter pylori flagellar motor from... -

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Entry
Database: EMDB / ID: EMD-48132
TitleIn situ structure of the Helicobacter pylori flagellar motor from the deletion of fapH with full length pflA
Map dataIn situ structure of the flagellar motor from the deletion fapH with full length of pflA
Sample
  • Cell: Helicobacter pylori
KeywordsFlagellar motor / Complex / H.pylori / Flagella / MOTOR PROTEIN
Biological speciesHelicobacter pylori (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 47.2 Å
AuthorsTachiyama S / Liu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI140444 United States
CitationJournal: PLoS Pathog / Year: 2025
Title: A Helicobacter pylori flagellar motor accessory is needed to maintain the barrier function of the outer membrane during flagellar rotation.
Authors: Kyle Rosinke / Shoichi Tachiyama / Jan Mrásek / Jun Liu / Timothy R Hoover /
Abstract: The Helicobacter pylori flagellar motor contains several accessory structures that are not found in the archetypal Escherichia coli and Salmonella enterica motors. H. pylori hp0838 encodes a ...The Helicobacter pylori flagellar motor contains several accessory structures that are not found in the archetypal Escherichia coli and Salmonella enterica motors. H. pylori hp0838 encodes a previously uncharacterized lipoprotein and is in an operon with flgP, which encodes a motor accessory protein. Deletion analysis of hp0838 in H. pylori B128 showed that the gene is not required for motility in soft agar medium, but the mutant displayed a reduced growth rate and an increased sensitivity to bacitracin, which is an antibiotic that is normally excluded by the outer membrane. Introducing a plasmid-borne copy of hp0838 into the H. pylori Δhp0838 mutant suppressed the fitness defect and antibiotic sensitivity of the strain. A variant of the Δhp0838 mutant containing a frameshift mutation in pflA, which resulted in paralyzed flagella, displayed wild-type growth rate and resistance to bacitracin, suggesting the fitness defect and antibiotic sensitivity of the Δhp0838 mutant are dependent on flagellar rotation. Comparative analysis of in-situ structures of the wild type and Δhp0838 mutant motors revealed the Δhp0838 mutant motor lacked a previously undescribed ring structure with 18-fold symmetry located near the outer membrane. Given its role in formation of the motor outer ring, HP0838 was designated FapH (flagellar accessory protein in Helicobacter pylori) and the motor accessory formed the protein was named the FapH ring. Our data suggest that the FapH ring helps to preserve outer membrane barrier function during flagellar rotation. Given that FapH homologs are present in many members of the phylum Campylobacterota, they may have similar roles in protecting the outer membrane from damage due to flagellar rotation in these bacteria.
History
DepositionDec 3, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48132.png

Downloads & links

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Map

FileDownload / File: emd_48132.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ structure of the flagellar motor from the deletion fapH with full length of pflA
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: 0.0552
Minimum - Maximum-0.5961483 - 0.75034815
Average (Standard dev.)0.0014488947 (±0.10014027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
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: The half map of the flagellar motor from...

Fileemd_48132_half_map_1.map
AnnotationThe half map of the flagellar motor from deletion fapH with full length of pflA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of the flagellar motor from...

Fileemd_48132_half_map_2.map
AnnotationThe half map of the flagellar motor from deletion fapH with full length of pflA
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

EntireName: Helicobacter pylori (bacteria)
Components
  • Cell: Helicobacter pylori

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Supramolecule #1: Helicobacter pylori

SupramoleculeName: Helicobacter pylori / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: B128

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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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.96 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: 47.2 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 7997
ExtractionNumber tomograms: 146 / Number images used: 534
Final angle assignmentType: OTHER

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