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- EMDB-39653: Subtomogram averaging of 8-nm-repeat triplet microtubule with inn... -

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Basic information

Entry
Database: EMDB / ID: EMD-39653
TitleSubtomogram averaging of 8-nm-repeat triplet microtubule with inner scaffold and complete C tubule within basal bodies from mouse ependymal cells
Map dataCryo-EM density map of 8-nm-repeat triplet microtubule with inner scaffold and complete C tubule from mouse ependymal cells
Sample
  • Cell: Primary culture of mouse ependymal cells
KeywordsBasal body / triplet microtubule / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 8.8 Å
AuthorsMa S / Guo Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371191 China
CitationJournal: To Be Published
Title: In situ cryo-electron tomography reveals the progressive biogenesis of basal bodies and cilia in mouse ependymal cells
Authors: Ma S / Li L / Li Z / Luo S / Liu Q / Du W / Qiu B / Zhu X / Gui M / Guo Q
History
DepositionApr 2, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39653.png

Downloads & links

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Map

FileDownload / File: emd_39653.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of 8-nm-repeat triplet microtubule with inner scaffold and complete C tubule from mouse ependymal cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.33 Å/pix.
x 276 pix.
= 918.528 Å		3.33 Å/pix.
x 276 pix.
= 918.528 Å		3.33 Å/pix.
x 276 pix.
= 918.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.523743 - 2.8682392
Average (Standard dev.)0.019846542 (±0.3334024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions276276276
Spacing276276276
CellA=B=C: 918.528 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39653_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39653_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Primary culture of mouse ependymal cells

EntireName: Primary culture of mouse ependymal cells
Components
  • Cell: Primary culture of mouse ependymal cells

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Supramolecule #1: Primary culture of mouse ependymal cells

SupramoleculeName: Primary culture of 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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.08 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 11794
ExtractionNumber tomograms: 177 / Number images used: 33516
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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