[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

TitleStructural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 4644, Year 2021
Publish dateJul 30, 2021
AuthorsGabriel Demo / Howard B Gamper / Anna B Loveland / Isao Masuda / Christine E Carbone / Egor Svidritskiy / Ya-Ming Hou / Andrei A Korostelev /
PubMed AbstractFrameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly ...Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly understood. We describe seven ~3.5-Å-resolution cryo-EM structures of 70S ribosome complexes, allowing visualization of elongation and translocation by the GTPase elongation factor G (EF-G). Four structures with a + 1-frameshifting-prone mRNA reveal that frameshifting takes place during translocation of tRNA and mRNA. Prior to EF-G binding, the pre-translocation complex features an in-frame tRNA-mRNA pairing in the A site. In the partially translocated structure with EF-G•GDPCP, the tRNA shifts to the +1-frame near the P site, rendering the freed mRNA base to bulge between the P and E sites and to stack on the 16S rRNA nucleotide G926. The ribosome remains frameshifted in the nearly post-translocation state. Our findings demonstrate that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
External linksNat Commun / PubMed:34330903 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.5 Å
Structure data

EMDB-22669: Cryo-EM map of pre-translocation non-frameshifting(CCA-A) complex (Structure I)
PDB-7k50: Pre-translocation non-frameshifting(CCA-A) complex (Structure I)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-22670: Cryo-EM map of mid-translocated non-frameshifting(CCA-A) complex with EF-G and GDPCP (Structure II)
PDB-7k51: Mid-translocated non-frameshifting(CCA-A) complex with EF-G and GDPCP (Structure II)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-22671: Cryo-EM map of near post-translocated non-frameshifting(CCA-A) complex with EF-G and GDPCP (Structure III)
PDB-7k52: Near post-translocated non-frameshifting(CCA-A) complex with EF-G and GDPCP (Structure III)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-22672: Cryo-EM map of pre-translocation +1-frameshifting(CCC-A) complex (Structure I-FS)
PDB-7k53: Pre-translocation +1-frameshifting(CCC-A) complex (Structure I-FS)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-22673: Cryo-EM of mid-translocated +1-frameshifting(CCC-A) complex with EF-G and GDPCP (Structure II-FS)
PDB-7k54: Mid-translocated +1-frameshifting(CCC-A) complex with EF-G and GDPCP (Structure II-FS)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-22674: Cryo-EM map of near post-translocated +1-frameshifting(CCC-A) complex with EF-G and GDPCP (Structure III-FS)
PDB-7k55: Near post-translocated +1-frameshifting(CCC-A) complex with EF-G and GDPCP (Structure III-FS)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-23528: Cryo-EM of pre-translocation rotated ribosome +1-frameshifting(CCC-A) complex (Structure Irot-FS)
PDB-7lv0: Pre-translocation rotated ribosome +1-frameshifting(CCC-A) complex (Structure Irot-FS)
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-FME:
N-FORMYLMETHIONINE

ChemComp-PRO:
PROLINE

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (strain k12) (bacteria)
  • escherichia coli k-12 (bacteria)
  • escherichia coli (E. coli)
KeywordsRIBOSOME / tRNA / TRANSLATION / EFG / EF-G

+
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