[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

TitleStructures of translationally inactive mammalian ribosomes.
Journal, issue, pagesElife, Vol. 7, Year 2018
Publish dateOct 24, 2018
AuthorsAlan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao /
PubMed AbstractThe cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.
External linksElife / PubMed:30355441 / PubMed Central
MethodsEM (single particle)
Resolution3.3 - 5.9 Å
Structure data

EMDB-9234:
Rabbit 80S ribosome with a P-site tRNA (unrotated state)
Method: EM (single particle) / Resolution: 5.9 Å

EMDB-9235:
Rabbit 80S ribosome with a P- and E-site tRNA
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-9236:
Rabbit 80S ribosome with a Z-site tRNA (unrotated state)
Method: EM (single particle) / Resolution: 4.2 Å

9237

6mtb

EMDB-9237, PDB-6mtb:
Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)
Method: EM (single particle) / Resolution: 3.6 Å

9239

6mtc

EMDB-9239, PDB-6mtc:
Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)
Method: EM (single particle) / Resolution: 3.4 Å

9240

6mtd

EMDB-9240, PDB-6mtd:
Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-9241:
Rabbit 80S ribosome with A/P and P/E tRNAs (rotated state)
Method: EM (single particle) / Resolution: 3.8 Å

9242

6mte

EMDB-9242, PDB-6mte:
Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

Source
  • oryctolagus cuniculus (rabbit)
  • unidentified (others)
  • Rabbit (rabbit)
  • Bovine (cattle)
KeywordsRIBOSOME / translation

+
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