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TitleThe structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1-17).
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 8, Year 2025
Publish dateApr 22, 2025
AuthorsKaroline Raulf / Timm O Koller / Bertrand Beckert / Alexander Lepak / Martino Morici / Mario Mardirossian / Marco Scocchi / Gert Bange / Daniel N Wilson /
PubMed AbstractProline-rich antimicrobial peptides (PrAMPs) are produced as part of the innate immune response of animals, insects, and plants. The well-characterized mammalian PrAMP bactenecin-5 (Bac5) has been ...Proline-rich antimicrobial peptides (PrAMPs) are produced as part of the innate immune response of animals, insects, and plants. The well-characterized mammalian PrAMP bactenecin-5 (Bac5) has been shown to help fight bacterial infection by binding to the bacterial ribosome and inhibiting protein synthesis. In the absence of Bac5-ribosome structures, the binding mode of Bac5 and exact mechanism of action has remained unclear. Here, we present a cryo-electron microscopy structure of Bac5 in complex with the 70S ribosome from the Gram-negative marine bacterium Vibrio natriegens. The structure shows that, despite sequence similarity to Bac7 and other type I PrAMPs, Bac5 displays a completely distinct mode of interaction with the ribosomal exit tunnel. Bac5 overlaps with the binding site of both A- and P-site transfer RNAs bound at the peptidyltransferase center, suggesting that this type I PrAMP can interfere with late stages of translation initiation as well as early stages of elongation. Collectively, our study presents a ribosome structure from V. natriegens, a fast-growing bacterium that has interesting biotechnological and synthetic biology applications, as well as providing additional insights into the diverse binding modes that type I PrAMPs can utilize to inhibit protein synthesis.
External linksNucleic Acids Res / PubMed:40331629 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 2.8 Å
Structure data

51946

9h90

EMDB-51946, PDB-9h90:
Cryo-EM structure of the Vibrio natrigens 30S ribosomal subunit in complex with spectinomycin.
Method: EM (single particle) / Resolution: 2.8 Å

51947

9h91

EMDB-51947, PDB-9h91:
Cryo-EM structure of the Vibrio natrigens 50S ribosomal subunit in complex with the proline-rich antimicrobial peptide Bac5(1-17).
Method: EM (single particle) / Resolution: 2.7 Å

Chemicals

ChemComp-SCM:
SPECTINOMYCIN / antibiotic*YM

ChemComp-HOH:
WATER

ChemComp-ZN:
Unknown entry

Source
  • vibrio natriegens (bacteria)
  • bos taurus (domestic cattle)
KeywordsRIBOSOME / Vibrio natriegens / Bac5 / Bactenecin 5 / 50S / V. natriegens

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