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- EMDB-40406: In situ structure of Helicobacter pylori flagellar motor from Pil... -

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Basic information

Entry
Database: EMDB / ID: EMD-40406
TitleIn situ structure of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant
Map dataA subtomogram averaged structure of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant
Sample
  • Cell: Helicobacter pylori
KeywordsH.pylori / Flagella / PilN / PilO / MOTOR PROTEIN
Biological speciesHelicobacter pylori G27 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 39.0 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)R01AI087846 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Bacterial flagella hijack type IV pili proteins to control motility.
Authors: Xiaolin Liu / Shoichi Tachiyama / Xiaotian Zhou / Rommel A Mathias / Sharmin Q Bonny / Mohammad F Khan / Yue Xin / Anna Roujeinikova / Jun Liu / Karen M Ottemann /
Abstract: Bacterial flagella and type IV pili (TFP) are surface appendages that enable motility and mechanosensing through distinct mechanisms. These structures were previously thought to have no components in ...Bacterial flagella and type IV pili (TFP) are surface appendages that enable motility and mechanosensing through distinct mechanisms. These structures were previously thought to have no components in common. Here, we report that TFP and some flagella share proteins PilO, PilN, and PilM, which we identified as part of the flagellar motor. mutants lacking PilO or PilN migrated better than wild type in semisolid agar because they continued swimming rather than aggregated into microcolonies, mimicking the TFP-regulated surface response. Like their TFP homologs, flagellar PilO/PilN heterodimers formed a peripheral cage that encircled the flagellar motor. These results indicate that PilO and PilN act similarly in flagella and TFP by differentially regulating motility and microcolony formation when bacteria encounter surfaces.
History
DepositionApr 8, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40406.png

Downloads & links

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Map

FileDownload / File: emd_40406.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA subtomogram averaged structure of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.59 Å/pix.
x 120 pix.
= 1031.04 Å		8.59 Å/pix.
x 120 pix.
= 1031.04 Å		8.59 Å/pix.
x 120 pix.
= 1031.04 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: 0.055
Minimum - Maximum-0.48530725 - 0.5677296
Average (Standard dev.)-0.000000000177953 (±0.08034866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 1031.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: An EM half map of Helicobacter pylori flagellar...

Fileemd_40406_half_map_1.map
AnnotationAn EM half map of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: An EM half map of Helicobacter pylori flagellar...

Fileemd_40406_half_map_2.map
AnnotationAn EM half map of Helicobacter pylori flagellar motor from PilN and PilO deletion mutant
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
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) / 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: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 6928
ExtractionNumber tomograms: 166 / Number images used: 478
Final angle assignmentType: OTHER

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