9H91

Cryo-EM structure of the Vibrio natrigens 50S ribosomal subunit in complex with the proline-rich antimicrobial peptide Bac5(1-17).

Summary for 9H91

• Entry DOI: 10.2210/pdb9h91/pdb
• EMDB information: 51947
• Descriptor: 50S ribosomal protein L32, 50S ribosomal protein L4, 50S ribosomal protein L6, ... (32 entities in total)
• Functional Keywords: vibrio natriegens, ribosome, bac5, bactenecin 5, 50s, v. natriegens
• Biological source: Vibrio natriegens; More
• Total number of polymer chains: 30
• Total formula weight: 1263552.96

Authors

Raulf, K.F.,Koller, T.O.,Beckert, B.,Morici, M.,Lepak, A.,Bange, G.,Wilson, D.N. (deposition date: 2024-10-29, release date: 2025-05-21)

Primary citation

Raulf, K.,Koller, T.O.,Beckert, B.,Lepak, A.,Morici, M.,Mardirossian, M.,Scocchi, M.,Bange, G.,Wilson, D.N.
The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1-17).
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: 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.

PubMed: 40331629
DOI: 10.1093/nar/gkaf324

Experimental method

ELECTRON MICROSCOPY (2.7 Å)