[English] 日本語
Yorodumi
- EMDB-39653: Subtomogram averaging of 8-nm-repeat triplet microtubule with inn... -

+
Open data


ID or keywords:

Loading...

-
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: 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
DepositionApr 2, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39653.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #1

Fileemd_39653_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39653_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Primary culture of mouse ependymal cells

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

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

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

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more