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- EMDB-64894: Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell -

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Basic information

Entry
Database: EMDB / ID: EMD-64894
TitleTomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
Map data
Sample
  • Cell: Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
KeywordsArchaea / STRUCTURAL PROTEIN
Biological speciesArchaea (unknown)
Methodelectron tomography / cryo EM
AuthorsImachi H / Hosogi N
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H04985 Japan
Japan Society for the Promotion of Science (JSPS)24H00582 Japan
Japan Society for the Promotion of Science (JSPS)22H04926 Japan
CitationJournal: bioRxiv / Year: 2025
Title: Eukaryotes' closest relatives are internally simple syntophic archaea.
Authors: Imachi H / Nobu MK / Ishii S / Hirakata Y / Hashiguchi H / Hosogi N / Ikuta T / Isaji Y / Miyata M / Miyazaki M / Morono Y / Murata K / Nakagawa S / Narita A / Ogawara M / Okada S / Saito Y ...Authors: Imachi H / Nobu MK / Ishii S / Hirakata Y / Hashiguchi H / Hosogi N / Ikuta T / Isaji Y / Miyata M / Miyazaki M / Morono Y / Murata K / Nakagawa S / Narita A / Ogawara M / Okada S / Saito Y / Sakai S / Shimamura S / Tahara YO / Takaki Y / Takano Y / Tasumi E / Uemtatsu K / Yoshimura T / Takai K
History
DepositionJun 2, 2025-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64894.png

Downloads & links

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Map

FileDownload / File: emd_64894.map.gz / Format: CCP4 / Size: 3.2 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.36 Å/pix.
x 2046 pix.
= 6878.652 Å		3.36 Å/pix.
x 294 pix.
= 988.428 Å		3.36 Å/pix.
x 2880 pix.
= 9682.56 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: 3.362 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2296.0 - 2286.0
Average (Standard dev.)83.896484000000001 (±223.664369999999991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-29400
Dimensions29428802046
Spacing28802942046
CellA: 9682.56 Å / B: 988.428 Å / C: 6878.652 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell

EntireName: Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
Components
  • Cell: Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell

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Supramolecule #1: Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell

SupramoleculeName: Tomogram of a Candidatus Margulisarchaeum peptidophila strain HC1 cell
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: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 15.824 µm / Nominal defocus min: 10.246 µm

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Image processing

Final reconstructionSoftware - Name: IMOD (ver. 4.9.12) / Number images used: 41
CTF correctionType: NONE

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