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Structure paper

TitleStructural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 10, Year 2025
Publish dateMay 22, 2025
AuthorsDisha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor Kaczmarczyk / Aneta Sroka / Masato Taoka / Yuko Nobe / Toshiaki Isobe / Susanne Paukner / Ella Zimmerman / Anat Bashan / Jan Potempa / Ada Yonath /
PubMed AbstractPorphyromonas 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 ...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.
External linksNucleic Acids Res / PubMed:40444637 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.1 Å
Structure data

52635

9i5t

EMDB-52635, PDB-9i5t:
50S subunit of P. gingivalis ribosome with Lefamulin
Method: EM (single particle) / Resolution: 2.6 Å

52640

9i5v

EMDB-52640, PDB-9i5v:
70S P. gingivalis ribosome erm-delta-porN strain
Method: EM (single particle) / Resolution: 2.7 Å

52641

9i5x

EMDB-52641, PDB-9i5x:
Porphyromonas gingivalis 70S ribosome (W83 Strain)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-52767: Focus refined 50S map of 70S P. gingivalis ribosome W83 strain
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-52768: Focus refined 30S body map of 70S P. gingivalis ribosome W83 strain
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-52770: Focus refined 30S head map of 70S P. gingivalis ribosome W83 strain
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-62B:
Lefamulin / medication, antibiotic*YM

ChemComp-K:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

Source
  • porphyromonas gingivalis (bacteria)
KeywordsRIBOSOME / antibiotics / macrolide-resistance / macrolide-resistant / Antibiotic / Lefamulin

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