[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

TitleSystematic studies of all PIH proteins in zebrafish reveal their distinct roles in axonemal dynein assembly.
Journal, issue, pagesElife, Vol. 7, Year 2018
Publish dateMay 9, 2018
AuthorsHiroshi Yamaguchi / Toshiyuki Oda / Masahide Kikkawa / Hiroyuki Takeda /
PubMed AbstractConstruction of motile cilia/flagella requires cytoplasmic preassembly of axonemal dyneins before transport into cilia. Axonemal dyneins have various subtypes, but the roles of each dynein subtype ...Construction of motile cilia/flagella requires cytoplasmic preassembly of axonemal dyneins before transport into cilia. Axonemal dyneins have various subtypes, but the roles of each dynein subtype and their assembly processes remain elusive in vertebrates. The PIH protein family, consisting of four members, has been implicated in the assembly of different dynein subtypes, although evidence for this idea is sparse. Here, we established zebrafish mutants of all four PIH-protein genes: , , , and , and analyzed the structures of axonemal dyneins in mutant spermatozoa by cryo-electron tomography. Mutations caused the loss of specific dynein subtypes, which was correlated with abnormal sperm motility. We also found organ-specific compositions of dynein subtypes, which could explain the severe motility defects of mutant Kupffer's vesicle cilia. Our data demonstrate that all vertebrate PIH proteins are differently required for cilia/flagella motions and the assembly of axonemal dyneins, assigning specific dynein subtypes to each PIH protein.
External linksElife / PubMed:29741156 / PubMed Central
MethodsEM (tomography)
Resolution41.7 - 45.1 Å
Structure data

EMDB-6954:
Doublet microtubule of zebrafish sperm axoneme, WT
Method: EM (tomography) / Resolution: 42.5 Å

EMDB-6955:
Doublet microtubule of zebrafish sperm axoneme, pih1d1_null mutant
Method: EM (tomography) / Resolution: 45.0 Å

EMDB-6956:
Doublet microtubule of zebrafish sperm axoneme, pih1d2_null mutant
Method: EM (tomography) / Resolution: 45.1 Å

EMDB-6957:
Doublet microtubule of zebrafish sperm axoneme, ktu_null mutant
Method: EM (tomography) / Resolution: 43.4 Å

EMDB-6958:
Doublet microtubule of zebrafish sperm axoneme, twister_null mutant
Method: EM (tomography) / Resolution: 43.7 Å

EMDB-6959:
Doublet microtubule of zebrafish sperm axoneme, pih1d2_null and ktu_null double_mutant, +OAD
Method: EM (tomography) / Resolution: 43.4 Å

EMDB-6960:
Doublet microtubule of zebrafish sperm axoneme, pih1d2_null and ktu_null double_mutant, -OAD
Method: EM (tomography) / Resolution: 41.7 Å

Source
  • Danio rerio (zebrafish)

+
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