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- EMDB-50315: Candidatus Methanosuratincola verstraetei strain LCB70 cell biolo... -

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Basic information

Entry
Database: EMDB / ID: EMD-50315
TitleCandidatus Methanosuratincola verstraetei strain LCB70 cell biology, an example of interaction between two cells
Map data
Sample
  • Cell: Candidatus Methanosuratincola verstraetei strain LCB70
KeywordsArchaea / phylum Thermoproteota / anaerobic archaea / thermophilic archaea / methanogen archaea / methanogenesis / archaea cell-cell interactions / UNKNOWN FUNCTION
Biological speciesCandidatus Methanosuratincola (archaea)
Methodelectron tomography / cryo EM
AuthorsPetrosian NS / Pilhofer M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)CoG 101000232European Union
CitationJournal: Nature / Year: 2024
Title: Cultivation and visualization of a methanogen of the phylum Thermoproteota.
Authors: Anthony J Kohtz / Nikolai Petrosian / Viola Krukenberg / Zackary J Jay / Martin Pilhofer / Roland Hatzenpichler /
Abstract: Methane is the second most abundant climate-active gas, and understanding its sources and sinks is an important endeavour in microbiology, biogeochemistry, and climate sciences. For decades, it was ...Methane is the second most abundant climate-active gas, and understanding its sources and sinks is an important endeavour in microbiology, biogeochemistry, and climate sciences. For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was taxonomically restricted to a metabolically specialized group of archaea, the Euryarchaeota. The discovery of marker genes for anaerobic alkane cycling in metagenome-assembled genomes obtained from diverse habitats has led to the hypothesis that archaeal lineages outside the Euryarchaeota are also involved in methanogenesis. Here we cultured Candidatus Methanosuratincola verstraetei strain LCB70, a member of the archaeal class Methanomethylicia (formerly Verstraetearchaeota) within the phylum Thermoproteota, from a terrestrial hot spring. Growth experiments combined with activity assays, stable isotope tracing, and genomic and transcriptomic analyses demonstrated that this thermophilic archaeon grows by means of methyl-reducing hydrogenotrophic methanogenesis. Cryo-electron tomography revealed that Ca. M. verstraetei are coccoid cells with archaella and chemoreceptor arrays, and that they can form intercellular bridges connecting two to three cells with continuous cytoplasm and S-layer. The wide environmental distribution of Ca. M. verstraetei suggests that they might play important and hitherto overlooked roles in carbon cycling within diverse anoxic habitats.
History
DepositionMay 15, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_50315.map.gz / Format: CCP4 / Size: 639.8 MB / Type: IMAGE STORED AS SIGNED BYTE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.04 Å/pix.
x 455 pix.
= 8208.2 Å
18.04 Å/pix.
x 1440 pix.
= 25977.602 Å
18.04 Å/pix.
x 1024 pix.
= 18472.961 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: 18.04 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)28.059626000000002 (±4.9854407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin208-208228
Dimensions14401024455
Spacing10241440455
CellA: 18472.96 Å / B: 25977.602 Å / C: 8208.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Candidatus Methanosuratincola verstraetei strain LCB70

EntireName: Candidatus Methanosuratincola verstraetei strain LCB70
Components
  • Cell: Candidatus Methanosuratincola verstraetei strain LCB70

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Supramolecule #1: Candidatus Methanosuratincola verstraetei strain LCB70

SupramoleculeName: Candidatus Methanosuratincola verstraetei strain LCB70
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Methanosuratincola (archaea)

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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: 6.5
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 180.0 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: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61
CTF correctionType: NONE

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