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Structure paper

TitleStructural studies on ribosomes of differentially macrolide-resistant strains.
Journal, issue, pagesLife Sci Alliance, Vol. 8, Issue 8, Year 2025
Publish dateJun 9, 2025
AuthorsAndré Rivalta / Aliza Fedorenko / Alexandre Le Scornet / Sophie Thompson / Yehuda Halfon / Elinor Breiner Goldstein / Sude Çavdaroglu / Tal Melenitzky / Disha-Gajanan Hiregange / Ella Zimmerman / Anat Bashan / Mee-Ngan Frances Yap / Ada Yonath /
PubMed AbstractAntimicrobial resistance is a major global health challenge, diminishing the efficacy of many antibiotics, including macrolides. In , an opportunistic pathogen, macrolide resistance is primarily ...Antimicrobial resistance is a major global health challenge, diminishing the efficacy of many antibiotics, including macrolides. In , an opportunistic pathogen, macrolide resistance is primarily mediated by Erm-family methyltransferases, which mono- or dimethylate A2058 in the 23S ribosomal RNA, reducing drug binding. Although macrolide-ribosome interactions have been characterized in nonpathogenic species, their structural basis in clinically relevant pathogens remains limited. In this study, we investigate the impact of -mediated resistance on drug binding by analyzing ribosomes from strains with varying levels of expression and activity. Using cryo-electron microscopy, we determined the high-resolution structures of solithromycin-bound ribosomes, including those with dimethylated A2058. Our structural analysis reveals the specific interactions that enable solithromycin binding despite double methylation and resistance, as corroborated by microbiological and biochemical data, suggesting that further optimization of ketolide-ribosome interactions could enhance macrolide efficacy against resistant strains.
External linksLife Sci Alliance / PubMed:40490363 / PubMed Central
MethodsEM (single particle)
Resolution2.07 - 2.39 Å
Structure data

EMDB-52642: Consensus map of the 70S ribosome of a MLSb sensitive S. aureus strain "KES34" in complex with solithromycin
Method: EM (single particle) / Resolution: 2.15 Å

EMDB-52647: Focused refinement of the large ribosomal subunit of a MLSb sensitive S. aureus strain "KES34" in complex with solithromycin
Method: EM (single particle) / Resolution: 2.07 Å

EMDB-52648: Postprocessed map of the focused refinement of the small ribosomal subunit body of a MLSb sensitive S. aureus strain "KES34"
Method: EM (single particle) / Resolution: 2.39 Å

EMDB-52649: Postprocessed map of the focused refinement of the small ribosomal subunit head of the MLSb sensitive S. aureus strain "KES34"
Method: EM (single particle) / Resolution: 2.39 Å

53066

9qeg

EMDB-53066, PDB-9qeg:
Cryo-EM structure of the 70S ribosome of a MLSb sensitive S. aureus strain "KES34" in complex with solithromycin
Method: EM (single particle) / Resolution: 2.21 Å

53067

9qeh

EMDB-53067, PDB-9qeh:
Cryo-EM structure of the A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
Method: EM (single particle) / Resolution: 2.08 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-EM1:
(3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a / antibiotic*YM

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

Source
  • staphylococcus aureus subsp. aureus usa300 (bacteria)
KeywordsRIBOSOME / resistance / rRNA / antibiotic

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