[English] 日本語
Yorodumi
- EMDB-63944: Microtubule doublet from wild-type mouse tracheal epithelial cells -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63944
TitleMicrotubule doublet from wild-type mouse tracheal epithelial cells
Map datalocal resolution map
Sample
  • Complex: microtubule doublet from wild-type mouse tracheal epithelial cells
Keywordscilia / microtubule doublets / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 20.7 Å
AuthorsZhang Y / Ni T / He M / Park HJ / Choi MJ / Cheung HO
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: The kinesin-4 protein KIF27 forms a cytoskeletal scaffold at the transition zone to promote motile cilia structural integrity.
Authors: Hyunji Park / Minjun Choi / Yu Zhang / Helen Oi-Lam Cheung / Shigeru Makino / Yoshiaki Yoshikawa / Haoran Qi / Zheng Liu / Guocheng Lan / Guoling Fu / Qian Wang / Shiny Shengzhen Guo / ...Authors: Hyunji Park / Minjun Choi / Yu Zhang / Helen Oi-Lam Cheung / Shigeru Makino / Yoshiaki Yoshikawa / Haoran Qi / Zheng Liu / Guocheng Lan / Guoling Fu / Qian Wang / Shiny Shengzhen Guo / Pengtao Liu / Zhen Liu / Shih-Chieh Ti / Won-Jing Wang / Xiang David Li / Tao Ni / Chi-Chung Hui / Mu He /
Abstract: Motile cilia are eukaryotic organelles with essential chemo- and mechanosensing functions across evolution, from single cell organisms to humans. Motile cilia of the mammalian nervous, respiratory, ...Motile cilia are eukaryotic organelles with essential chemo- and mechanosensing functions across evolution, from single cell organisms to humans. Motile cilia of the mammalian nervous, respiratory, and reproductive systems are characterized by unique motility proteins to generate fluid flow essential for transporting metabolites and removing mucus. The molecular mechanism underlying motile cilia assembly remains unknown. Here, we use high-resolution imaging, proteomics, in situ cryotomography, and single-molecule motility assays to identify mammalian KIF27, a motor protein of the Kinesin-4 family and homologue of the Hedgehog pathway regulator COS2/KIF7, as a key regulator of motile cilia assembly in vivo. We show that KIF27 promotes the integrity of the transition zone (TZ), a diffusion barrier situated at the cilium base. Loss of KIF27 results in specific and profound defects in axonemal structure and disrupts cilia beating, which collectively lead to organismal phenotypes that recapitulate primary ciliary dyskinesia (PCD). We show that the motile properties of KIF27 are dispensable for its function in motile cilia assembly. Instead, KIF27 acts as a microtubule scaffold to regulate the TZ architecture and enable correct ciliary incorporation of motility-generating proteins. Given that KIF27 orthologues exist in different evolutionarily lineages, we propose that the ancestral activity of KIF27/KIF7 kinesins was to form a microtubule-associated scaffold for protein-protein interactions pertinent to cilia formation and signaling. The transition-zone-associated KIF27 activities may represent a general building principle for the motile cilia assembly in diverse species and cell types.
History
DepositionMar 25, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63944.png

Downloads & links

-
Map

FileDownload / File: emd_63944.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.83 Å/pix.
x 120 pix.
= 580.08 Å		4.83 Å/pix.
x 120 pix.
= 580.08 Å		4.83 Å/pix.
x 120 pix.
= 580.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.06285363 - 0.0851405
Average (Standard dev.)-0.000005031451 (±0.0191289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 580.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_63944_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map generates from reconstruction map

Fileemd_63944_half_map_1.map
Annotationhalf map generates from reconstruction map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map generates from reconstruction map

Fileemd_63944_half_map_2.map
Annotationhalf map generates from reconstruction map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : microtubule doublet from wild-type mouse tracheal epithelial cells

EntireName: microtubule doublet from wild-type mouse tracheal epithelial cells
Components
  • Complex: microtubule doublet from wild-type mouse tracheal epithelial cells

-
Supramolecule #1: microtubule doublet from wild-type mouse tracheal epithelial cells

SupramoleculeName: microtubule doublet from wild-type mouse tracheal epithelial cells
type: complex / 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
Component:
ConcentrationFormulaName
30.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
25.0 mMNaClSodium chloride
5.0 mMMgSO4magnesium sulfate
1.0 mMEGTAethylene glycol tetraacetic acid
0.1 mMEDTAEthylenediaminetetraacetic acid

Details: 30 mM HEPES, 25 mM NaCl, 5 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA, 0.1 mM DTT, protease inhibitor, pH 7.3
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 310.15 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.0 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: 4.0 µm / Nominal magnification: 53000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsFalcon 4i selectris X energy filter
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v4) / Number subtomograms used: 2089
ExtractionNumber tomograms: 8 / Number images used: 3126
CTF correctionSoftware: (Name: emClarity (ver. 1.6.1), Dynamo, RELION (ver. 4))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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