[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

TitleCoupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 3751, Year 2020
Publish dateJul 27, 2020
AuthorsJelena Micic / Yu Li / Shan Wu / Daniel Wilson / Beril Tutuncuoglu / Ning Gao / John L Woolford /
PubMed AbstractThe protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring ...The protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring of the Rpf2 subcomplex containing 5S rRNA, rpL5, rpL11, Rpf2 and Rrs1, which initially docks onto the flexible domain V of rRNA at earlier stages of assembly. In this work, we tested the function of the C-terminal domain (CTD) of Rpf2 during these anchoring steps, by truncating this extension and assaying effects on middle stages of subunit maturation. The rpf2Δ255-344 mutation affects proper folding of rRNA helices H68-70 during anchoring of the Rpf2 subcomplex. In addition, several assembly factors (AFs) are absent from pre-ribosomes or in altered conformations. Consequently, major remodeling events fail to occur: rotation of the 5S RNP, maturation of the peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), and export of assembling subunits to the cytoplasm.
External linksNat Commun / PubMed:32719344 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 6.0 Å
Structure data

30108

6m62

EMDB-30108, PDB-6m62:
Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state.
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-30109:
Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisiae Sda1 depletion strain, E2 state
Method: EM (single particle) / Resolution: 4.8 Å

EMDB-30110:
Eukaryotic pre-60S ribosomal subunit from Saccharomyces cerevisiae rpf2delta255-344 strain, C1 state at 6 Angstroms resolution.
Method: EM (single particle) / Resolution: 6.0 Å

EMDB-30111:
Eukaryotic pre-60S ribosomal subunit from Saccharomyces cerevisiae rpf2delta255-344 strain, C2 state at 5.9 Angstroms resolution
Method: EM (single particle) / Resolution: 5.9 Å

EMDB-30112:
Cryo-EM structure of pre-60S ribosomal subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C3 state at 3.9 Angstroms resolution.
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-30113:
Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisiae Sda1 depletion strain, E1 state
Method: EM (single particle) / Resolution: 5.9 Å

Chemicals

ChemComp-ZN:
Unknown entry

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

ChemComp-MG:
Unknown entry

Source
  • saccharomyces cerevisiae s288c (yeast)
  • Baker's yeast (brewer's yeast)
KeywordsRIBOSOME / pre-60s / Rpf2

+
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