[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

TitleStructure-based design and synthesis of group A streptogramins that bind to the nascent peptide exit tunnel of the ribosome.
Journal, issue, pagesEur J Med Chem, Vol. 316, Page 118947, Year 2026
Publish dateMay 9, 2026
AuthorsIsabel J Lee / Qi Li / Tushar Raskar / Jenna Pellegrino / Andrew K Ecker / Sara Y Howard / James S Fraser / Ian B Seiple /
PubMed AbstractNatural products and their derivatives have long served as powerful tools for treating bacterial infections, but the rise of antibiotic resistance threatens their continued effectiveness. Targeted ...Natural products and their derivatives have long served as powerful tools for treating bacterial infections, but the rise of antibiotic resistance threatens their continued effectiveness. Targeted structural modification of existing classes of antibiotics is an effective strategy to overcome resistance and extend clinical utility. The development of group A streptogramins that overcome acetyltransferase resistance, a pervasive resistance mechanism to the class, is an example of successful implementation of this strategy. However, the synthetic chemistry to reach these new analogs was limited in its ability to access modifications at the C4 position on the scaffold, a promising modification site that produced the most potent streptogramin to date. Here, we report the development of a modified route to group A streptogramins that enables access to a broad diversity of functionality at C4. Using cryo-EM data to guide structural modifications, we synthesize several series of C4-modified group A streptogramins with sidechains designed to make binding contacts with the exit tunnel of the ribosome. We identify multiple analogs that are active against multidrug-resistant bacteria, including strains that are resistant to macrolides, β-lactams, vancomycin, and first-generation streptogramins. We structurally characterize the binding of two analogs to the bacterial ribosome, revealing new π-stacking interactions between the C4 sidechain and the non-canonical U1782-U2586 base pair. These findings demonstrate how structure-guided drug design can drive the development of next-generation antibiotics and increase the therapeutic potential of the streptogramin class.
External linksEur J Med Chem / PubMed:42214237
MethodsEM (single particle)
Resolution2.49 Å
Structure data

75389

10qm

EMDB-75389, PDB-10qm:
E.coli 50S ribosomal subunit bound to compound 48a
Method: EM (single particle) / Resolution: 2.49 Å

Chemicals

ChemComp-MG:
Unknown entry

PDB-1c7k:
CRYSTAL STRUCTURE OF THE ZINC PROTEASE

ChemComp-NA:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / 50S subunit / antibiotic

+
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