[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

TitleElectron cryotomography of intact motile cilia defines the basal body to axoneme transition.
Journal, issue, pagesJ Cell Biol, Vol. 219, Issue 1, Year 2020
Publish dateJan 6, 2020
AuthorsGarrett A Greenan / Ronald D Vale / David A Agard /
PubMed AbstractCells use motile cilia to generate force in the extracellular space. The structure of a cilium can be classified into three subdomains: the intracellular basal body (BB) that templates cilium ...Cells use motile cilia to generate force in the extracellular space. The structure of a cilium can be classified into three subdomains: the intracellular basal body (BB) that templates cilium formation, the extracellular axoneme that generates force, and the transition zone (TZ) that bridges them. While the BB is composed of triplet microtubules (TMTs), the axoneme is composed of doublet microtubules (DMTs), meaning the cilium must convert between different microtubule geometries. Here, we performed electron cryotomography to define this conversion, and our reconstructions reveal identifying structural features of the BB, TZ, and axoneme. Each region is distinct in terms of microtubule number and geometry, microtubule inner proteins, and microtubule linkers. TMT to DMT conversion occurs within the BB, and microtubule geometry changes to axonemal by the end of the TZ, followed by the addition of axoneme-specific components essential for cilium motility. Our results provide the highest-resolution images of the motile cilium to date and reveal how BBs template axonemes.
External linksJ Cell Biol / PubMed:31874113 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution30.7 - 35.6 Å
Structure data

EMDB-20674:
Nascent axoneme from bovine respiratory epithelial cells
Method: EM (subtomogram averaging) / Resolution: 35.6 Å

EMDB-20675:
Whole-population average of the first 800 nm of the bovine respiratory epithelium
Method: EM (subtomogram averaging) / Resolution: 30.7 Å

EMDB-20676:
Average of the basal body from bovine respiratory cilia
Method: EM (subtomogram averaging) / Resolution: 31.5 Å

EMDB-20679:
Average of the transition zone from bovine respiratory cilia
Method: EM (subtomogram averaging) / Resolution: 31.5 Å

EMDB-20680:
Average of the proximal axoneme from bovine respiratory cilia
Method: EM (subtomogram averaging) / Resolution: 35.1 Å

EMDB-20681:
Average of the proximal basal body from bovine respiratory cilia
Method: EM (subtomogram averaging) / Resolution: 33.2 Å

EMDB-20683:
Average of the mid basal body from bovine respiratory cilia
Method: EM (subtomogram averaging) / Resolution: 33.2 Å

EMDB-20684:
Average of the distal basal body from bovine respiratory cilia
Method: EM (subtomogram averaging) / Resolution: 32.3 Å

EMDB-20685:
Average of the TZ linker from bovine respiratory cilia
Method: EM (subtomogram averaging) / Resolution: 33.2 Å

Source
  • Bos taurus (cattle)

+
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