[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

TitleVisualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes.
Journal, issue, pagesCell, Vol. 171, Issue 7, Page 1599-1610.e14, Year 2017
Publish dateDec 14, 2017
AuthorsLukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann /
PubMed AbstractEukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance.
External linksCell / PubMed:29245012 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.24 - 4.3 Å
Structure data

3888

6em3

EMDB-3888: State A (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
PDB-6em3: State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 4.2 Å

3889

6em4

EMDB-3889: State B (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
PDB-6em4: State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 4.1 Å

3890

6em5

EMDB-3890: State D (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
PDB-6em5: State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 4.2 Å

3891

6elz

EMDB-3891, PDB-6elz:
State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-3892:
State F (Rix1-TAP Rpf2-Flag) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 3.3 Å

3893

6em1

EMDB-3893, PDB-6em1:
State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Method: EM (single particle) / Resolution: 3.6 Å

PDB-6emf:
Crystal structure of Rrp1 from Chaetomium thermophilum in space group C2
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-6emg:
Crystal structure of Rrp1 from Chaetomium thermophilum in space group P6322
Method: X-RAY DIFFRACTION / Resolution: 2.24 Å

PDB-6en7:
Crystal structure of the ribosome assembly factor Nsa1
Method: X-RAY DIFFRACTION / Resolution: 2.403 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-PRO:
PROLINE

ChemComp-HOH:
WATER

ChemComp-PO4:
PHOSPHATE ION

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • chaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) (fungus)
KeywordsRIBOSOME / Large Subunit Biogenesis Nucleolus / Ribosome biogenesis / translation / CHAPERONE / biogenesis

+
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