9TEX

Dal2 bound to the Escherichia coli 70S ribosome

This is a non-PDB format compatible entry.

Summary for 9TEX

• Entry DOI: 10.2210/pdb9tex/pdb
• EMDB information: 55845
• Descriptor: 23S rRNA, Large ribosomal subunit protein bL34, Large ribosomal subunit protein bL35, ... (56 entities in total)
• Functional Keywords: dal2, pramp, translation, inhibitor, initiation, ncpet, ribosome, cryo-em, antibiotic
• Biological source: Escherichia coli BW25113; More
• Total number of polymer chains: 55
• Total formula weight: 2169613.93

Authors

Berger, M.J.,Safdari, H.A.,Wilson, D.N. (deposition date: 2025-11-26, release date: 2026-05-13, Last modification date: 2026-07-22)

Primary citation

Huang, W.,Berger, M.J.,Safdari, H.A.,Klepacki, D.,Paternoga, H.,Baliga, C.,Wilson, D.N.,Vazquez-Laslop, N.,Mankin, A.S.
Flipping antimicrobial peptides in the exit tunnel of the bacterial ribosome.
Nat Commun, 17:-, 2026

PubMed Abstract: Proline-rich antimicrobial peptides (PrAMPs) kill bacteria by binding in the ribosomal nascent peptide exit tunnel. Type II PrAMPs bind in an orientation matching that of the nascent protein, trap the release factors and arrest ribosomes at stop codons. Conversely, Type I PrAMPs bind in an opposite orientation: their N-terminus invades the peptidyl transferase center arresting translation at start codons. Here, by mining the genome databases, we identify a number of PrAMPs with high sequence similarity to the Type II PrAMP Drosocin. Notably, many of the new PrAMPs do not stall ribosomes at stop codons, but act as Type I PrAMPs arresting translation at start codons. Structural analysis shows that such peptides bind with a Type I orientation. Minimal alterations in the peptide structure can flip the orientation of the PrAMP in the exit tunnel, switching the mechanism of translation inhibition. Altering the mode of binding and action of a PrAMP by only few mutations could be exploited by the host to combat newly emerging bacterial pathogens.

PubMed: 42236475
DOI: 10.1038/s41467-026-74007-x

Experimental method

ELECTRON MICROSCOPY (2.54 Å)