[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

TitleDocking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro.
Journal, issue, pagesJ Cell Sci, Vol. 129, Issue 8, Page 1547-1551, Year 2016
Publish dateApr 15, 2016
AuthorsToshiyuki Oda / Tatsuki Abe / Haruaki Yanagisawa / Masahide Kikkawa /
PubMed AbstractThe docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to ...The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs can bind to DMTs and porcine microtubules with 24-nm periodicities even in the absence of the docking complexin vitro Using cryo-electron tomography and structural labeling, we observed that the docking complex took an unexpectedly flexible conformation and did not lie along the length of DMTs. In the absence of docking complex, ODAs were released from the DMT at relatively low ionic strength conditions, suggesting that the docking complex strengthens the electrostatic interactions between the ODA and DMT. Based on these results, we conclude that the docking complex serves as a flexible stabilizer of the ODA rather than as a molecular ruler.
External linksJ Cell Sci / PubMed:26933181
MethodsEM (subtomogram averaging)
Resolution45.0 - 49.0 Å
Structure data

EMDB-6504:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 47.0 Å

EMDB-6505:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 48.0 Å

EMDB-6506:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 45.0 Å

EMDB-6507:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 49.0 Å

EMDB-6508:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 47.0 Å

EMDB-6509:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 46.0 Å

EMDB-6510:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 47.0 Å

EMDB-6511:
Docking complex-independent alignment of outer dynein arms with 24-nm periodicity
Method: EM (subtomogram averaging) / Resolution: 49.0 Å

Source
  • Chlamydomonas reinhardtii (plant)

+
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