9H90
Cryo-EM structure of the Vibrio natrigens 30S ribosomal subunit in complex with spectinomycin.
Summary for 9H90
| Entry DOI | 10.2210/pdb9h90/pdb |
| EMDB information | 51946 |
| Descriptor | 30S ribosomal protein S21, 16S ribosomal RNA, 30S ribosomal protein S20, ... (20 entities in total) |
| Functional Keywords | vibrio natriegens, ribosome, bac5, bactenecin 5, 50s, v. natriegens |
| Biological source | Vibrio natriegens More |
| Total number of polymer chains | 18 |
| Total formula weight | 735536.82 |
| 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 Cited by 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: 40331629DOI: 10.1093/nar/gkaf324 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.8 Å) |
Structure validation
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