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- EMDB-15989: cryo-tomogram of a Ca. L. ossiferum cell -

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Basic information

Entry
Database: EMDB / ID: EMD-15989
Titlecryo-tomogram of a Ca. L. ossiferum cell
Map data
Sample
  • Cell: Ca. L. ossiferum
Biological speciesunidentified (others)
Methodelectron tomography / cryo EM
AuthorsRodrigues-Oliveira T / Wollweber F / Ponce-Toledo R / Xu J / Rittmann S / Klingl A / Pilhofer M / Schleper C
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)695192European Union
European Research Council (ERC)101000232European Union
CitationJournal: Nature / Year: 2023
Title: Actin cytoskeleton and complex cell architecture in an Asgard archaeon.
Authors: Thiago Rodrigues-Oliveira / Florian Wollweber / Rafael I Ponce-Toledo / Jingwei Xu / Simon K-M R Rittmann / Andreas Klingl / Martin Pilhofer / Christa Schleper /
Abstract: Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of ...Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated, but never visualized. Here we describe a highly enriched culture of 'Candidatus Lokiarchaeum ossiferum', a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7-14 days, reaches cell densities of up to 5 × 10 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying 'Ca. L. ossiferum' cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin-one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.
History
DepositionOct 20, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_15989.map.gz / Format: CCP4 / Size: 562.5 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 18.04 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)24.568676 (±3.8818266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208208-200
Dimensions14401024400
Spacing10241440400
CellA: 18472.96 Å / B: 25977.602 Å / C: 7216.0005 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ca. L. ossiferum

EntireName: Ca. L. ossiferum
Components
  • Cell: Ca. L. ossiferum

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Supramolecule #1: Ca. L. ossiferum

SupramoleculeName: Ca. L. ossiferum / type: cell / ID: 1 / Parent: 0 / Details: organism name: Ca. Lokiarchaeum ossiferum
Source (natural)Organism: unidentified (others)

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE
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 (6k x 4k) / Average electron dose: 2.3 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 61

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