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- EMDB-63320: Tomogram of a Candidatus Flexarchaeum multiprotrusionis strain SC... -

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Basic information

Entry
Database: EMDB / ID: EMD-63320
TitleTomogram of a Candidatus Flexarchaeum multiprotrusionis strain SC1 cell
Map dataTomogram of a Candidatus Flexarchaeum multiprotrusionis strain SC1 cell
Sample
  • Cell: Candidatus Flexarchaeum multiprotrusionis strain SC1
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_63320.png

Downloads & links

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Map

FileDownload / File: emd_63320.map.gz / Format: CCP4 / Size: 693.5 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of a Candidatus Flexarchaeum multiprotrusionis strain SC1 cell
Voxel sizeX=Y=Z: 12.38 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)69.715040000000002 (±6.0420413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-441-19260
Dimensions10002020360
Spacing20201000360
CellA: 25007.6 Å / B: 12380.0 Å / C: 4456.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Candidatus Flexarchaeum multiprotrusionis strain SC1

EntireName: Candidatus Flexarchaeum multiprotrusionis strain SC1
Components
  • Cell: Candidatus Flexarchaeum multiprotrusionis strain SC1

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Supramolecule #1: Candidatus Flexarchaeum multiprotrusionis strain SC1

SupramoleculeName: Candidatus Flexarchaeum multiprotrusionis strain SC1 / 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 R3.5/1 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 15 nm

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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 electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.2 µm / Calibrated defocus min: 3.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 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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