[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

TitleH/ACA snR30 snoRNP guides independent 18S rRNA subdomain formation.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 4720, Year 2025
Publish dateMay 21, 2025
AuthorsPaulina Fischer / Matthias Thoms / Benjamin Lau / Timo Denk / Maria Kuvshinova / Otto Berninghausen / Dirk Flemming / Ed Hurt / Roland Beckmann /
PubMed AbstractRibosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, ...Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, composed of pre-18S rRNA, ribosomal S-proteins, U3 snoRNA, and ~70 assembly factors. However, how numerous snoRNAs control pre-rRNA modification and folding during early maturation events remains unclear. We identify snR30 (human U17), the only essential H/ACA snoRNA in yeast, which binds with Cbf5-Gar1-Nop10-Nhp2 to a pre-18S rRNA subdomain containing platform helices and ES6 of the 40S central domain. Integration into the 90S is blocked by RNA hybridization with snR30. The snoRNP complex coordinates the recruitment of early assembly factors Krr1-Utp23-Kri1 and ribosomal proteins uS11-uS15, enabling isolated subdomain assembly. Krr1-dependent release of snR30 culminates in integration of the platform into the 90S. Our study reveals the essential role of snR30 in chaperoning central domain formation as a discrete assembly unit externalized from the pre-ribosomal core.
External linksNat Commun / PubMed:40399280 / PubMed Central
MethodsEM (single particle)
Resolution2.83 - 3.93 Å
Structure data

EMDB-50647: Stalled 90S - Utp23-Krr1-deltaC3 - Consensus refinement
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-50648: Stalled 90S - Utp23-Krr1-deltaC3 - Head-Kre33 module - local refinement
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-50649: Stalled 90S - Utp23-Krr1-deltaC3 - Krr1 - local refinement
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-50650: Stalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-50651: Stalled 90S - Utp23-Krr1-deltaC3 - Utp10 - local refinement
Method: EM (single particle) / Resolution: 3.59 Å

EMDB-50652: Stalled 90S - Utp23-Krr1-deltaC3 - Utp12 - local refinement
Method: EM (single particle) / Resolution: 3.38 Å

EMDB-50653: Stalled 90S - Utp23-Krr1-deltaC3 - Utp20 - local refinement
Method: EM (single particle) / Resolution: 3.23 Å

EMDB-50654: Stalled 90S - Utp23-Krr1-deltaC3 - UTP-A - local refinement
Method: EM (single particle) / Resolution: 3.11 Å

EMDB-50958: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local refinement
Method: EM (single particle) / Resolution: 2.83 Å

EMDB-50959: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 5' HACA - local refinement
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-50960: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - Platform module - local refinement
Method: EM (single particle) / Resolution: 2.94 Å

EMDB-50961: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - Consensus refinement
Method: EM (single particle) / Resolution: 2.89 Å

50964

9g25

EMDB-50964, PDB-9g25:
snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3
Method: EM (single particle) / Resolution: 2.89 Å

EMDB-50967: snR30 snoRNP - Class 1 - Utp23-Krr1-wt
Method: EM (single particle) / Resolution: 3.92 Å

50968

9g28

EMDB-50968, PDB-9g28:
snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-50969: snR30 snoRNP - Class 2 - Utp23-Krr1-wt
Method: EM (single particle) / Resolution: 3.93 Å

50991

9g33

EMDB-50991, PDB-9g33:
Stalled 90S - Utp23-Krr1-deltaC3
Method: EM (single particle) / Resolution: 3.05 Å

Chemicals

ChemComp-ZN:
Unknown entry

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

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsRIBOSOME / 90S / pre-ribosome / snoRNA / snR30 / snoRNP / ribosome biogenesis / H/ACA / 18S rRNA

+
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