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- EMDB-54242: Cryo-tomogram of FIB-milled Tetrahymena cell -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54242
TitleCryo-tomogram of FIB-milled Tetrahymena cell
Map data
Sample
  • Cell: Tetrahymena thermophile
Keywordscentriole / basal body / centrosome / STRUCTURAL PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodelectron tomography / cryo EM
AuthorsCai B / Xu JW / Luo L / Aarts E / Leitner A / Ishikawa T / Beltro P / Pilhofer M / Wieczorek M
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
ETH ZurichETH-22 22-1 Switzerland
Swiss National Science Foundation320030-231677 Switzerland
Swiss National Science FoundationIZLIZ3 200294 Switzerland
CitationJournal: To Be Published
Title: Structure and assembly of the A-C linker connecting microtubule triplets in centrioles
Authors: Cai B / Xu JW / Luo L / Aarts E / Leitner A / Ishikawa T / Beltro P / Pilhofer M / Wieczorek M
History
DepositionJul 2, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54242.png

Downloads & links

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Map

FileDownload / File: emd_54242.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.04 Å/pix.
x 400 pix.
= 7216. 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

Histogram

Histogram (log scale)
Minimum - Maximum-1069.0 - 942.0
Average (Standard dev.)9.802237999999999 (±49.719574000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208208-193
Dimensions14401024400
Spacing10241440400
CellA: 18472.96 Å / B: 25977.602 Å / C: 7216.0005 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: demonised tomogram

Fileemd_54242_additional_1.map
Annotationdemonised tomogram
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrahymena thermophile

EntireName: Tetrahymena thermophile
Components
  • Cell: Tetrahymena thermophile

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Supramolecule #1: Tetrahymena thermophile

SupramoleculeName: Tetrahymena thermophile / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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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
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1500 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 4000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 3.17 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 41
CTF correctionType: NONE

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