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- EMDB-70016: Focus-refined structures of FlgY spokes in the Helicobacter pylor... -

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Entry
Database: EMDB / ID: EMD-70016
TitleFocus-refined structures of FlgY spokes in the Helicobacter pylori flagellar motor in situ
Map dataFocus-refined structures of FlgY spokes in the Helicobacter pylori flagellar motor
Sample
  • Cell: Helicobacter pylori
KeywordsH. pylori / Flagella / Complex / Flagellar motor / MOTOR PROTEIN
Biological speciesHelicobacter pylori G27 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 10.5 Å
AuthorsTachiyama S / Liu J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI132828 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: FlgY, PflA, and PflB form a spoke-ring network in the high-torque flagellar motor of .
Authors: Shoichi Tachiyama / Kyle Rosinke / Mohammad F Khan / Xiaotian Zhou / Yue Xin / Jack M Botting / Jian Yue / Anna Roujeinikova / Timothy R Hoover / Jun Liu /
Abstract: has evolved distinct flagellar motility to colonize the human stomach. Rotation of the flagella is driven by one of the largest known bacterial flagellar motors. In addition to the core motor ... has evolved distinct flagellar motility to colonize the human stomach. Rotation of the flagella is driven by one of the largest known bacterial flagellar motors. In addition to the core motor components found in and , the flagellar motor in possesses many accessories that enable the bacteria to penetrate the gastric mucus layer. Here, we utilize cryoelectron tomography with molecular genetics and biochemical approaches to characterize three accessory proteins, FlgY, PflA, and PflB, and their roles in flagellar assembly and motility. Comparative analyses of in situ flagellar motor structures from , , and mutants and wild-type reveal that FlgY forms a 13-fold proximal spoke-ring around the MS-ring and that PflA and PflB form an 18-fold distal spoke-ring enclosing 18 torque-generating stator complexes. We build a pseudoatomic model of the motor by leveraging AlphaFold-predicted structures, protein-protein interactions, and motor structures. Our model suggests that the FlgY spoke-ring functions as a bearing around the rotating MS-ring and as a template for stabilizing the PflA-PflB spoke-ring, thus enabling the recruitment of 18 stator complexes for high-torque generation. Overall, our study sheds light on how this spoke-ring network between the MS-ring and stator complexes enables the unique motility of . As these accessory proteins are conserved in the phylum Campylobacterota, our findings apply broadly to a better understanding of how polar flagella help bacteria thrive in gastric and enteric niches.
History
DepositionApr 3, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70016.png

Downloads & links

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Map

FileDownload / File: emd_70016.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocus-refined structures of FlgY spokes in the Helicobacter pylori flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.15 Å/pix.
x 220 pix.
= 472.56 Å		2.15 Å/pix.
x 220 pix.
= 472.56 Å		2.15 Å/pix.
x 220 pix.
= 472.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.148 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0292
Minimum - Maximum-0.11396685 - 0.16086403
Average (Standard dev.)0.000000000014675 (±0.020199984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions220220220
Spacing220220220
CellA=B=C: 472.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of focus-refined structures of FlgY spokes...

Fileemd_70016_half_map_1.map
AnnotationHalf map of focus-refined structures of FlgY spokes in the Helicobacter pylori flagellar motor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of focus-refined structures of FlgY spokes...

Fileemd_70016_half_map_2.map
AnnotationHalf map of focus-refined structures of FlgY spokes in the Helicobacter pylori flagellar motor
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 G27 (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-PROPANE

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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: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 9638
ExtractionNumber tomograms: 567 / Number images used: 1635
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER

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