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- EMDB-63285: A tomogram of deuterosome-dependent basal body biogenesis in mous... -

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Basic information

Entry
Database: EMDB / ID: EMD-63285
TitleA tomogram of deuterosome-dependent basal body biogenesis in mouse ependymal cells
Map data
Sample
  • Cell: Mouse ependymal cells
Keywordsbasal body / deuterosome / mouse ependymal cells / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsMa S / Li Z / Luo S / Du W / Guo Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371191 China
CitationJournal: Nat Commun / Year: 2025
Title: In situ cryo-electron tomography reveals the progressive biogenesis of basal bodies and cilia.
Authors: Ma S / Li L / Li Z / Luo S / Liu Q / Du W / Qiu B / Gui M / Zhu X / Guo Q
History
DepositionJan 27, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63285.png

Downloads & links

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Map

FileDownload / File: emd_63285.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
26.62 Å/pix.
x 150 pix.
= 3993.6 Å		26.62 Å/pix.
x 720 pix.
= 19169.281 Å		26.62 Å/pix.
x 512 pix.
= 13631.488 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: 26.624 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.6566372 - 0.22612022
Average (Standard dev.)-0.000008343116 (±0.021412658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720512150
Spacing512720150
CellA: 13631.488 Å / B: 19169.281 Å / C: 3993.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mouse ependymal cells

EntireName: Mouse ependymal cells
Components
  • Cell: Mouse ependymal cells

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Supramolecule #1: Mouse ependymal cells

SupramoleculeName: Mouse ependymal cells / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 190
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.8 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 reconstructionNumber images used: 49
CTF correctionType: NONE

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