9I5T

50S subunit of P. gingivalis ribosome with Lefamulin

This is a non-PDB format compatible entry.

Summary for 9I5T

• Entry DOI: 10.2210/pdb9i5t/pdb
• EMDB information: 52635
• Descriptor: Large ribosomal subunit protein bL28, 23S rRNA, 5S rRNA, ... (38 entities in total)
• Functional Keywords: ribosome, antibiotics, macrolide-resistance
• Biological source: Porphyromonas gingivalis; More
• Total number of polymer chains: 32
• Total formula weight: 1381236.13

Authors

Hiregange, D.G.,Bashan, A.,Yonath, A. (deposition date: 2025-01-28, release date: 2025-08-20)

Primary citation

Hiregange, D.G.,Samiya, S.,Mizgalska, D.,Ben-Zeev, E.,Waghalter, M.,Rivalta, A.,Rajan, K.S.,Halfon, Y.,Breiner-Goldstein, E.,Kaczmarczyk, I.,Sroka, A.,Taoka, M.,Nobe, Y.,Isobe, T.,Paukner, S.,Zimmerman, E.,Bashan, A.,Potempa, J.,Yonath, A.
Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its propensity to form biofilms pose a challenge to effective treatment. To explore therapeutic avenues, we studied the high-resolution cryogenic electron microscope structures of ribosomes from the wild-type P. gingivalis W83 and the macrolide-resistant mutant strain ermΔporN. The structural analysis revealed unique features primarily at the ribosome periphery. Together with the distinctive distribution of ribosomal RNA modifications, these findings offer insights into the therapeutical potential, such as creation of novel therapeutic compounds inhibiting the specific cellular functions of the P. gingivalis ribosomes. Moreover, the high-resolution structure of the ermΔporN ribosome in its complex with the approved antibiotic lefamulin suggests its repurposing against P. gingivalis. Furthermore, we provide a foundation for additional effective strategies to treat periodontitis and associated systemic diseases.

PubMed: 40444637
DOI: 10.1093/nar/gkaf458

Experimental method

ELECTRON MICROSCOPY (2.6 Å)