Fig. 4: Cryo-EM structure of rumicidin-2 and its interactions with the bacterial ribosome.
From: Rumicidins are a family of mammalian host-defense peptides plugging the 70S ribosome exit tunnel
a Cross-section of the 70S initiation complex (50S subunit in blue, 30S subunit in yellow, fMet-tRNAfMet in green) with the rumicidin-2 (red) bound in the exit tunnel (PDB ID 9D89, EMD-46632). b Binding site of rumicidin-2 relative to fMet-tRNAfMet (green), uL4 (orange) and uL22 (cyan) ribosomal proteins. c Coulomb potential map of rumicidin-2 (gray mesh) determined with cryo-EM and a corresponding atomic model (red) of the well-resolved P12-R27 fragment of rumicidin-2. d Structural comparison of rumicidin-2 (red, PDB ID: 9D89) with Bac7 (green, PDB ID: 5HAU), Onc112 (yellow, PDB ID: 4Z8C), and Tur1A (blue, PDB ID: 6FKR) in the ribosomal exit tunnel. Similarly to other oncocin-like AMPs, rumicidins bind to the ribosomal peptide exit tunnel in the extended conformation and are oriented with the N-terminal region towards PTC. e Interactions of the central part of rumicidin-2 (captioned in red) with 23S rRNA (nucleotides are captioned in light blue, stacking interactions are shown as black arrows, hydrogen bonds are shown as dotted lines). f Interactions of rumicidin-2 (captioned in red) with uL4 protein (residues Arg61, Arg67 captioned in orange), uL22 (residues Lys90 captioned in cyan) and 23S rRNA (A751 captioned in blue).
