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- EMDB-63282: A tomogram of basal body docked into plasma membrane and templati... -

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Basic information

Entry
Database: EMDB / ID: EMD-63282
TitleA tomogram of basal body docked into plasma membrane and templating a cilium 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 in mouse ependymal cells.
Authors: Shanshan Ma / Luan Li / Zhixun Li / Shenjia Luo / Qi Liu / Wenjing Du / Benhua Qiu / Miao Gui / Xueliang Zhu / Qiang Guo /
Abstract: Cilia, essential organelles for cell motility and signaling, comprise an axoneme extended from the basal body (BB). The assembly process of BBs and axonemes during ciliogenesis, however, remains ...Cilia, essential organelles for cell motility and signaling, comprise an axoneme extended from the basal body (BB). The assembly process of BBs and axonemes during ciliogenesis, however, remains largely unknown due to the lack of structural information. Here, we leverage in-situ cryo-electron tomography to capture within mouse ependymal cells the dynamic processes of BB biogenesis and multiciliogenesis at various stages. This approach enables 3D visualization of the complete motile machinery, revealing the continuous microtubule-based scaffold from BBs to axonemes at sub-nanometer resolution with unprecedented structural details. Furthermore, we elucidate along BBs and cilia heterogeneous landscapes of microtubule-binding proteins underlying the establishment of structural periodicity and diverse subregions. Notably, the chronological binding patterns of microtubule-inner proteins (e.g., CEP41) correlate with the progressive assembly of ciliary beating machinery. We also resolve a substructure that borders the BB and the axoneme. Our findings provide key insights into intricate orchestrations during ciliogenesis.
History
DepositionJan 27, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63282.png

Downloads & links

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Map

FileDownload / File: emd_63282.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-0.20489627 - 0.17147735
Average (Standard dev.)0.000016831982 (±0.021666765)
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 {'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 (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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