[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

TitleRegulation of the macrolide resistance ABC-F translation factor MsrD.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 3891, Year 2023
Publish dateJul 1, 2023
AuthorsCorentin R Fostier / Farès Ousalem / Elodie C Leroy / Saravuth Ngo / Heddy Soufari / C Axel Innis / Yaser Hashem / Grégory Boël /
PubMed AbstractAntibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we ...Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex.
External linksNat Commun / PubMed:37393329 / PubMed Central
MethodsEM (single particle)
Resolution2.97 - 3.3 Å
Structure data

13805

7q4k

EMDB-13805, PDB-7q4k:
Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-13806: 50S LSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-13807: 30S-body SSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Method: EM (single particle) / Resolution: 3.08 Å

EMDB-13808: 30S-head SSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ERY:
ERYTHROMYCIN A / antibiotic*YM / Erythromycin

ChemComp-HOH:
WATER / Water

Source
  • escherichia coli (E. coli)
  • streptococcus pneumoniae (bacteria)
  • escherichia coli k-12 (bacteria)
KeywordsRIBOSOME / protein synthesis / antibiotic resistance / ARE ABC-F protein family / leader peptide / cryo-EM

+
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