[English] 日本語
Yorodumi
- EMDB-64774: Cryo-EM density map of the 96-nm repeat of the human respiratory ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64774
TitleCryo-EM density map of the 96-nm repeat of the human respiratory doublet microtubule
Map data
Sample
  • Complex: Doublet microtubule and associated proteins
Keywordshuman respiratory doublet microtubule / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.7 Å
AuthorsYang S / Gui M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2026
Title: Loss-of-function variants in ODAD1 disrupt ODA docking and induce actin cytoskeletal remodeling in primary ciliary dyskinesia.
Authors: Chunxiao Huo / Ting Luo / Shuo Yang / Yuan Jiang / Mengzhe Guo / Feng Yang / Zhangqi Xu / Junhua Xia / Lei Wu / Weize Xu / Miao Gui / Tianhua Zhou / Shanshan Xie /
Abstract: Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder characterized by defective mucociliary clearance due to impaired motile cilia function. Outer dynein arm docking complex ...Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder characterized by defective mucociliary clearance due to impaired motile cilia function. Outer dynein arm docking complex subunit 1 (ODAD1) encodes a structural component of the outer dynein arm docking complex (ODA-DC), which is crucial for effective ciliary beating. However, the full spectrum of ODAD1-associated pathogenesis remains incompletely defined. Here, we identified one novel homozygous loss-of-function ODAD1 variant, c.705_706insGCAG, and a recurrent homozygous splicing variant, c.-41-2A > C, in seven unrelated patients. These patients exhibited hallmark PCD symptoms with reduced nasal nitric oxide levels and situs inversus. Patient-derived nasal epithelial cells and air‒liquid interface (ALI) cultures exhibited a markedly reduced ciliary beating frequency and severe motility defects. Transmission electron microscopy and cryo-electron microscopy showed a complete loss of outer dynein arms and docking complexes, with variant-specific ultrastructural abnormalities. Unexpectedly, ODAD1 deficiency also led to reduced multiciliated cells (MCCs) abundance, misoriented basal bodies, and impaired multiciliogenesis. Proteomic profiling and immunostaining revealed prominent actin cytoskeletal remodeling, including aberrant F-actin bundling throughout the epithelial layers. Pharmacological inhibition of actin polymerization using cytochalasin B partially rescued the abundance of MCCs and multiciliogenesis, indicating that actin dysregulation is a modifiable consequence of ODAD1 loss. Finally, lentiviral re-expression of wild-type ODAD1 in patient-derived organoids restored ODA assembly and rescued coordinated ciliary beating, confirming the pathogenicity of the identified variants. Our data reveal a dual role for ODAD1 in regulating both axonemal structure and epithelial cytoskeletal integrity and identify actin dysregulation as a previously unrecognized, targetable pathological mechanism of ODAD1-associated PCD.
History
DepositionMay 23, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64774.png

Downloads & links

-
Map

FileDownload / File: emd_64774.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.86 Å/pix.
x 704 pix.
= 1309.44 Å		1.86 Å/pix.
x 704 pix.
= 1309.44 Å		1.86 Å/pix.
x 704 pix.
= 1309.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.013658977 - 0.031310067
Average (Standard dev.)0.0004829755 (±0.0024171693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions704704704
Spacing704704704
CellA=B=C: 1309.4401 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64774_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_64774_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_64774_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64774_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_64774_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Doublet microtubule and associated proteins

EntireName: Doublet microtubule and associated proteins
Components
  • Complex: Doublet microtubule and associated proteins

-
Supramolecule #1: Doublet microtubule and associated proteins

SupramoleculeName: Doublet microtubule and associated proteins / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
EMDB ID:

26624

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4034
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: ANGULAR RECONSTITUTION
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