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- EMDB-43432: Pseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-43432
TitlePseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion mutant
Map dataPseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion mutant
Sample
  • Organelle or cellular component: Delta-PilB upper and mid cages
KeywordsType IV Pilus Machine / Pseudomonas aeruginosa / cryo-electron tomography / CELL ADHESION
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 29.4 Å
AuthorsGuo S / Liu J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2024
Title: PilY1 regulates the dynamic architecture of the type IV pilus machine in Pseudomonas aeruginosa.
Authors: Shuaiqi Guo / Yunjie Chang / Yves V Brun / P Lynne Howell / Lori L Burrows / Jun Liu /
Abstract: Type IV pili (T4P) produced by the pathogen Pseudomonas aeruginosa play a pivotal role in adhesion, surface motility, biofilm formation, and infection in humans. Despite the significance of T4P as a ...Type IV pili (T4P) produced by the pathogen Pseudomonas aeruginosa play a pivotal role in adhesion, surface motility, biofilm formation, and infection in humans. Despite the significance of T4P as a potential therapeutic target, key details of their dynamic assembly and underlying molecular mechanisms of pilus extension and retraction remain elusive, primarily due to challenges in isolating intact T4P machines from the bacterial cell envelope. Here, we combine cryo-electron tomography with subtomogram averaging and integrative modelling to resolve in-situ architectural details of the dynamic T4P machine in P. aeruginosa cells. The T4P machine forms 7-fold symmetric cage-like structures anchored in the cell envelope, providing a molecular framework for the rapid exchange of major pilin subunits during pilus extension and retraction. Our data suggest that the T4P adhesin PilY1 forms a champagne-cork-shaped structure, effectively blocking the secretin channel in the outer membrane whereas the minor-pilin complex in the periplasm appears to contact PilY1 via the central pore of the secretin gate. These findings point to a hypothetical model where the interplay between the secretin protein PilQ and the PilY1-minor-pilin priming complex is important for optimizing conformations of the T4P machine in P. aeruginosa, suggesting a gate-keeping mechanism that regulates pilus dynamics.
History
DepositionJan 17, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43432.png

Downloads & links

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Map

FileDownload / File: emd_43432.map.gz / Format: CCP4 / Size: 2.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 86 pix.
= 369.456 Å		4.3 Å/pix.
x 86 pix.
= 369.456 Å		4.3 Å/pix.
x 86 pix.
= 369.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.31896284 - 0.2876282
Average (Standard dev.)0.0017866665 (±0.032801624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions868686
Spacing868686
CellA=B=C: 369.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Pseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion...

Fileemd_43432_half_map_1.map
AnnotationPseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion mutant, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion...

Fileemd_43432_half_map_2.map
AnnotationPseudomonas aeruginosa Type IV Pilus Machine, PilY1 deletion mutant, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Delta-PilB upper and mid cages

EntireName: Delta-PilB upper and mid cages
Components
  • Organelle or cellular component: Delta-PilB upper and mid cages

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Supramolecule #1: Delta-PilB upper and mid cages

SupramoleculeName: Delta-PilB upper and mid cages / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas aeruginosa (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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 29.4 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 2182
ExtractionNumber tomograms: 283 / Number images used: 5214
Final angle assignmentType: OTHER

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