[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural diversity of axonemes across mammalian motile cilia.
Journal, issue, pagesNature, Year 2025
Publish dateJan 1, 2025
AuthorsMiguel Ricardo Leung / Chen Sun / Jianwei Zeng / Jacob R Anderson / Qingwei Niu / Wei Huang / Willem E M Noteborn / Alan Brown / Tzviya Zeev-Ben-Mordehai / Rui Zhang /
PubMed AbstractReproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the ...Reproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the axoneme is available for the alga Chlamydomonas reinhardtii, structures of mammalian axonemes are incomplete. Furthermore, we do not fully understand how molecular structures of axonemes vary across motile-ciliated cell types in the body. Here we use cryoelectron microscopy, cryoelectron tomography and proteomics to resolve the 96-nm modular repeat of axonemal doublet microtubules (DMTs) from both sperm flagella and epithelial cilia of the oviduct, brain ventricles and respiratory tract. We find that sperm DMTs are the most specialized, with epithelial cilia having only minor differences across tissues. We build a model of the mammalian sperm DMT, defining the positions and interactions of 181 proteins including 34 newly identified proteins. We elucidate the composition of radial spoke 3 and uncover binding sites of kinases associated with regeneration of ATP and regulation of ciliary motility. We discover a sperm-specific, axoneme-tethered T-complex protein ring complex (TRiC) chaperone that may contribute to construction or maintenance of the long flagella of mammalian sperm. We resolve axonemal dyneins in their prestroke states, illuminating conformational changes that occur during ciliary movement. Our results illustrate how elements of chemical and mechanical regulation are embedded within the axoneme, providing valuable resources for understanding the aetiology of ciliopathy and infertility, and exemplifying the discovery power of modern structural biology.
External linksNature / PubMed:39743588
MethodsEM (subtomogram averaging) / EM (single particle)
Resolution3.52 - 10.0 Å
Structure data

EMDB-45677: 96-nm repeat of axonemal doublet microtubules from porcine oviduct cilia, subtomogram average segment 1 of 4
Method: EM (subtomogram averaging) / Resolution: 9.6 Å

EMDB-45678: 96-nm repeat of axonemal doublet microtubules from porcine oviduct cilia, subtomogram average segment 2 of 4
Method: EM (subtomogram averaging) / Resolution: 9.4 Å

EMDB-45679: 96-nm repeat of axonemal doublet microtubules from porcine oviduct cilia, subtomogram average segment 3 of 4
Method: EM (subtomogram averaging) / Resolution: 9.3 Å

EMDB-45680: 96-nm repeat of axonemal doublet microtubules from porcine oviduct cilia, subtomogram average segment 4 of 4
Method: EM (subtomogram averaging) / Resolution: 10.0 Å

EMDB-45683: Dynein motor inner dynein arm subform c (IDAc) from bovine Fallopian tube
Method: EM (single particle) / Resolution: 7.92 Å

EMDB-45697: Radial Spoke 3 from bovine Fallopian tube, stalk and head
Method: EM (single particle) / Resolution: 9.95 Å

EMDB-45699: Dynein motor inner dynein arm subform c (IDAc) from Porcine brain ventricles
Method: EM (single particle) / Resolution: 7.8 Å

EMDB-45713: Radial Spoke 3 from Pocine brain ventricles, stalk and head
Method: EM (single particle) / Resolution: 9.72 Å

EMDB-45714: The nexin-dynein regulatory complex (N-DRC) from human fallopian tube, distal part
Method: EM (single particle) / Resolution: 6.77 Å

EMDB-45725: Radial Spoke 3 from human fallopian tube, stalk and head
Method: EM (single particle) / Resolution: 5.83 Å

EMDB-45783: Composite map of bovine Fallopian tube cilia in 96nm repeat
Method: EM (single particle) / Resolution: 3.52 Å

EMDB-45784: Composite map of porcine brain ventricle cilia in 96nm repeat
Method: EM (single particle) / Resolution: 3.65 Å

EMDB-45785: Composite map of human Fallopian tube cilia in 96nm repeat
Method: EM (single particle) / Resolution: 3.56 Å

EMDB-45790: Dynein motor inner dynein arm subform f (IDAf) from human fallopian tube
Method: EM (single particle) / Resolution: 9.26 Å

45801

9cpb

EMDB-45801: Cryo-EM structure of bovine Fallopian tube cilia doublet microtubule (48-nm periodicity)
PDB-9cpb: Atomic model of bovine Fallopian tube cilia doublet microtubule (48-nm periodicity)
Method: EM (single particle) / Resolution: 3.52 Å

45802

9cpc

EMDB-45802: Cryo-EM structure of porcine brain ventricles cilia doublet microtubule (48-nm periodicity)
PDB-9cpc: Atomic model of porcine brain ventricles cilia doublet microtubule (48-nm periodicity)
Method: EM (single particle) / Resolution: 3.65 Å

Chemicals

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

Source
  • sus scrofa (pig)
  • bos taurus (cattle)
  • Homo sapiens (human)
KeywordsSTRUCTURAL PROTEIN / axoneme / cilia / microtubule / dynein / Fallopian tube / doublet microtubule (DMT) / brain ventricle

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more