[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

TitleImpact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.
Journal, issue, pagesPLoS One, Vol. 18, Issue 3, Page e0283698, Year 2023
Publish dateMar 30, 2023
AuthorsGisela Pöll / Joachim Griesenbeck / Herbert Tschochner / Philipp Milkereit /
PubMed AbstractRpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work ...RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work in yeast indicated that S0-cluster assembly is required for the stabilisation and maturation of SSU precursors at specific post-nucleolar stages. Here, we analysed the role of S0-cluster formation for rRNA folding. Structures of SSU precursors isolated from yeast S0-cluster expression mutants or control strains were analysed by cryogenic electron microscopy. The obtained resolution was sufficient to detect individual 2'-O-methyl RNA modifications using an unbiased scoring approach. The data show how S0-cluster formation enables the initial recruitment of the pre-rRNA processing factor Nob1 in yeast. Furthermore, they reveal hierarchical effects on the pre-rRNA folding pathway, including the final maturation of the central pseudoknot. Based on these structural insights we discuss how formation of the S0-cluster determines at this early cytoplasmic assembly checkpoint if SSU precursors further mature or are degraded.
External linksPLoS One / PubMed:36996028 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 4.3 Å
Structure data

EMDB-16346: Enp1TAP-S21_A, consensus Refinement
Method: EM (single particle) / Resolution: 2.9 Å

16347

8c00

EMDB-16347, PDB-8c00:
Enp1TAP-S21_A population of yeast small ribosomal subunit precursors depleted of rpS21/eS21
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-16348: Enp1TAP_A, consensus refinement
Method: EM (single particle) / Resolution: 2.7 Å

16349

8c01

EMDB-16349: Enp1TAP_A population of yeast small ribosomal subunit precursors, multibody refinement
PDB-8c01: Enp1TAP_A population of yeast small ribosomal subunit precursors
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-16350: Enp1TAP_B, multibody refinement
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-16351: Enp1TAP_B, consensus refinement
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-16352: Slx9TAP-S21_A
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-16358: Enp1TAP_B, body 1
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-16359: Enp1TAP_B, body 2
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-16360: Enp1TAP_A, body 1
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-16361: Enp1TAP_A, body 2
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-16362: Enp1TAP-S21_A, body 1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-16363: Enp1TAP-S21_A, body 2
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • baker's yeast (brewer's yeast)
KeywordsRIBOSOME / ribosomal assembly state

+
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