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- EMDB-63317: Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell -

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Basic information

Entry
Database: EMDB / ID: EMD-63317
TitleTomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
Map dataTomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
Sample
  • Cell: Candidatus Margulisarchaeum peptidophila strain HC1
Keywordscell / archaeia / cryo-electron tomography / CELL INVASION
Biological speciesArchaea (unknown)
Methodelectron tomography / cryo EM
AuthorsMurata K / Kayama Y / Imachi H
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121005 Japan
CitationJournal: Biorxiv / Year: 2025
Title: Eukaryotes' closest relatives are internally simple syntrophic archaea.
Authors: Imachi H / Nobu MK / Ishii S / Hirakata Y / Ikuta T / Isaji Y / Miyata M / Miyazaki M / Morono Y / Murata K / Nakagawa S / Ogawara M / Okada S / Saito Y / Sakai S / Shimamura S / Tahara YO / ...Authors: Imachi H / Nobu MK / Ishii S / Hirakata Y / Ikuta T / Isaji Y / Miyata M / Miyazaki M / Morono Y / Murata K / Nakagawa S / Ogawara M / Okada S / Saito Y / Sakai S / Shimamura S / Tahara YO / Takaki Y / Takano Y / Tasumi E / Uematsu K / Yoshimura T / Takai K
History
DepositionJan 29, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63317.png

Downloads & links

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Map

FileDownload / File: emd_63317.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
Voxel sizeX=Y=Z: 12.38 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-3.9030426 (±7.0861087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin175175-99
Dimensions13501350200
Spacing13501350200
CellA: 16713.0 Å / B: 16713.0 Å / C: 2476.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Candidatus Margulisarchaeum peptidophila strain HC1

EntireName: Candidatus Margulisarchaeum peptidophila strain HC1
Components
  • Cell: Candidatus Margulisarchaeum peptidophila strain HC1

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Supramolecule #1: Candidatus Margulisarchaeum peptidophila strain HC1

SupramoleculeName: Candidatus Margulisarchaeum peptidophila strain HC1 / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Archaea (unknown)

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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
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 85.0 K / Max: 85.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 61 / Average exposure time: 6.31 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 8.4 µm / Calibrated defocus min: 8.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 9.0 µm / Nominal magnification: 19500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 5.1) / Number images used: 61

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