[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

TitleThe binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly.
Journal, issue, pagesNucleic Acids Res, Year 2024
Publish dateDec 10, 2024
AuthorsDominic Arpin / Armando Palacios / Kaustuv Basu / Joaquin Ortega /
PubMed AbstractThe intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play ...The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play pivotal roles in completing the maturation of the functional sites in the 45S particle. In this work, we found that RbgA and YphC can independently bind the 45S particle with high affinity, but when RbgA binds first to the particle, it significantly increases the binding affinity of YphC. Using cryo-electron microscopy, we determined that the changes exerted by RbgA and YphC when binding independently closely resemble those observed when the two factors bind to the 45S particle simultaneously. However, the structural analysis revealed that RbgA binding causes a conformational change that uncovers the binding site for YphC, thus increasing its binding affinity. We concluded that the functional interplay between RbgA and YphC primarily revolves around one factor promoting the binding of the other, rather than the binding of the two factors inducing entirely new conformational changes compared with those induced by the factors individually. These results highlight the synergic mechanism between two essential assembly factors, underscoring the intricate mechanism bacteria use to maximize the efficiency of the ribosome assembly process.
External linksNucleic Acids Res / PubMed:39658043
MethodsEM (single particle)
Resolution2.7 - 3.3 Å
Structure data

EMDB-44832: 50S assembly intermediate 45SYphC Class 1
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-44836: 50S assembly intermediate 45SYphC Class 2
Method: EM (single particle) / Resolution: 2.8 Å

44849

9bs0

EMDB-44849, PDB-9bs0:
YphC-treated 45SYphC particle. Class 5
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-44851: YphC-treated 45SYphC particle. Class 1
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-44852: YphC-treated 45SYphC particle. Class 2
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-44853: YphC-treated 45SYphC particle. Class 3
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-44854: YphC-treated 45SYphC particle. Class 4
Method: EM (single particle) / Resolution: 3.0 Å

44869

9bsl

EMDB-44869, PDB-9bsl:
45SRbgA particle in complex with RbgA and YphC. Class A
Method: EM (single particle) / Resolution: 3.1 Å

44871

9bss

EMDB-44871, PDB-9bss:
45SRbgA particle in complex with RbgA and YphC. Class B
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

Source
  • Bacillus subtilis (bacteria)
  • bacillus subtilis subsp. subtilis str. 168 (bacteria)
KeywordsRIBOSOME / ribosome assembly / YphC

+
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