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- EMDB-19886: Distinct life cycle stages of an ectosymbiotic DPANN archaeon -

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Basic information

Entry
Database: EMDB / ID: EMD-19886
TitleDistinct life cycle stages of an ectosymbiotic DPANN archaeon
Map dataCryo-electron tomogram of Nanobdella aerobiophila (free single cell).
Sample
  • Cell: Free single cell of Nanobdella aerobiophila MJ1
Keywordsextracellular appendages / contact-dependent interactions / attachment organelle / CELL CYCLE
Biological speciesNanobdella aerobiophila (archaea)
Methodelectron tomography / cryo EM / Resolution: 10.71 Å
AuthorsGaisin VA / Wolferen M / Albers SA / Pilhofer M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)CoG 101000232European Union
CitationJournal: ISME J / Year: 2024
Title: Distinct life cycle stages of an ectosymbiotic DPANN archaeon.
Authors: Vasil A Gaisin / Marleen van Wolferen / Sonja-Verena Albers / Martin Pilhofer /
Abstract: DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell-cell interactions remains largely unknown. We ...DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell-cell interactions remains largely unknown. We applied live-cell imaging and cryo-electron tomography to the DPANN archaeon Nanobdella aerobiophila and its host, revealing two distinct life cycle stages. Free cells possess archaella and are motile. Ectobiotic cells are intimately linked with the host through an elaborate attachment organelle. Our data suggest that free cells may actively seek a new host, while the ectobiotic state is adapted to mediate intricate interaction with the host.
History
DepositionMar 20, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19886.png

Downloads & links

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Map

FileDownload / File: emd_19886.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryo-electron tomogram of Nanobdella aerobiophila (free single cell).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.71 Å/pix.
x 400 pix.
= 4284. Å		10.71 Å/pix.
x 1440 pix.
= 15422.4 Å		10.71 Å/pix.
x 1024 pix.
= 10967.04 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.71 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-896.0 - 581.0
Average (Standard dev.)4.430388 (±15.057077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-209208-200
Dimensions14401024400
Spacing10241440400
CellA: 10967.04 Å / B: 15422.4 Å / C: 4284.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Free single cell of Nanobdella aerobiophila MJ1

EntireName: Free single cell of Nanobdella aerobiophila MJ1
Components
  • Cell: Free single cell of Nanobdella aerobiophila MJ1

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Supramolecule #1: Free single cell of Nanobdella aerobiophila MJ1

SupramoleculeName: Free single cell of Nanobdella aerobiophila MJ1 / type: cell / ID: 1 / Parent: 0
Details: Cryo-electron tomogram of ectosymbiotic DPANN archaeon Nanobdella aerobiophila MJ1. A single cell without the host.
Source (natural)Organism: Nanobdella aerobiophila (archaea) / Strain: MJ1

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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: 2.5
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Pressure: 0.037 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 80 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average exposure time: 1.1 sec. / Average electron dose: 2.574 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: 8.0 µm / Nominal magnification: 33000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.71 Å / Software - Name: IMOD (ver. 4.11.12) / Number images used: 61

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