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- EMDB-15988: In situ sub-tomogram average of Ca. L. ossiferum actin filament -

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Basic information

Entry
Database: EMDB / ID: EMD-15988
TitleIn situ sub-tomogram average of Ca. L. ossiferum actin filament
Map data
Sample
  • Complex: Ca. L. ossiferum actin
Biological speciesunidentified (others)
Methodsubtomogram averaging / cryo EM / Resolution: 24.5 Å
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

emd_15988.png

Downloads & links

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Map

FileDownload / File: emd_15988.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 128 pix.
= 342.784 Å		2.68 Å/pix.
x 128 pix.
= 342.784 Å		2.68 Å/pix.
x 128 pix.
= 342.784 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.678 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-2.593196 - 7.593982
Average (Standard dev.)0.09533745 (±0.70636946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 342.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15988_msk_1.map
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Half map: #1

Fileemd_15988_half_map_1.map
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Half map: #2

Fileemd_15988_half_map_2.map
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Sample components

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Entire : Ca. L. ossiferum actin

EntireName: Ca. L. ossiferum actin
Components
  • Complex: Ca. L. ossiferum actin

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Supramolecule #1: Ca. L. ossiferum actin

SupramoleculeName: Ca. L. ossiferum actin / type: complex / ID: 1 / Chimera: Yes / 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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 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 - Helical parameters - Δz: 27.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 24.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 12585
ExtractionNumber tomograms: 56 / Number images used: 13569
Final angle assignmentType: MAXIMUM LIKELIHOOD

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