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- EMDB-25217: Slice of a cryo-electron tomogram of PhiPA3-infected Pseudomonas ... -

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Basic information

Entry
Database: EMDB / ID: EMD-25217
TitleSlice of a cryo-electron tomogram of PhiPA3-infected Pseudomonas aeruginosa cell at 70 mpi (Cell 3)
Map dataSlice of a cryo-electron tomogram of PhiPA3-infected Pseudomonas aeruginosa cell at 70 mpi (Cell 3)
Sample
  • Cell: Pseudomonas aeruginosa infected with bacteriophage PhiPA3 at 75 mpi
KeywordsBacteriophage / Phage Bouquet / Jumbo phage infection / VIRUS
Biological speciesPseudomonas aeruginosa PA1 (bacteria)
Methodelectron tomography / cryo EM
AuthorsKhanna K / Villa E
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104556 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129245 United States
National Science Foundation (NSF, United States)DBI 1920374 United States
CitationJournal: Sci Adv / Year: 2022
Title: Subcellular organization of viral particles during maturation of nucleus-forming jumbo phage.
Authors: Vorrapon Chaikeeratisak / Kanika Khanna / Katrina T Nguyen / MacKennon E Egan / Eray Enustun / Emily Armbruster / Jina Lee / Kit Pogliano / Elizabeth Villa / Joe Pogliano /
Abstract: Many eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages are generally assumed to assemble randomly throughout the host cell cytoplasm. Here, we ...Many eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages are generally assumed to assemble randomly throughout the host cell cytoplasm. Here, we show that viral particles of nucleus-forming jumbo phage PhiPA3 assemble into a unique structure inside cells we term phage bouquets. We show that after capsids complete DNA packaging at the surface of the phage nucleus, tails assemble and attach to capsids, and these particles accumulate over time in a spherical pattern, with tails oriented inward and the heads outward to form bouquets at specific subcellular locations. Bouquets localize at the same fixed distance from the phage nucleus even when it is mispositioned, suggesting an active mechanism for positioning. These results mark the discovery of a pathway for organizing mature viral particles inside bacteria and demonstrate that nucleus-forming jumbo phages, like most eukaryotic viruses, are highly spatially organized during all stages of their lytic cycle.
History
DepositionOct 27, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25217.png

Downloads & links

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Map

FileDownload / File: emd_25217.map.gz / Format: CCP4 / Size: 531.1 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationSlice of a cryo-electron tomogram of PhiPA3-infected Pseudomonas aeruginosa cell at 70 mpi (Cell 3)
Voxel sizeX=Y=Z: 22.46 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)32.027630000000002 (±8.504201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00176
Dimensions12801236352
Spacing12361280352
CellA: 27760.559 Å / B: 28748.799 Å / C: 7905.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Pseudomonas aeruginosa infected with bacteriophage PhiPA3 at 75 mpi

EntireName: Pseudomonas aeruginosa infected with bacteriophage PhiPA3 at 75 mpi
Components
  • Cell: Pseudomonas aeruginosa infected with bacteriophage PhiPA3 at 75 mpi

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Supramolecule #1: Pseudomonas aeruginosa infected with bacteriophage PhiPA3 at 75 mpi

SupramoleculeName: Pseudomonas aeruginosa infected with bacteriophage PhiPA3 at 75 mpi
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas aeruginosa PA1 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 2000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Scios. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 60

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