8CEP

Kasugamycin bound to the 30S body

Summary for 8CEP

• Entry DOI: 10.2210/pdb8cep/pdb
• Related: 8CA7 8CAI 8CAM 8CAZ 8CEU 8CF1 8CF8 8CGD 8CGI 8CGJ 8CGK 8CGR 8CGU 8CGV
• EMDB information: 16520 16526 16530 16536 16612 16613 16615 16620 16641 16644 16645 16646 16650 16651 16652
• Related PRD ID: PRD_000193
• Descriptor: 16S rRNA, Small ribosomal subunit protein uS17, Small ribosomal subunit protein bS18, ... (19 entities in total)
• Functional Keywords: antibiotic, ribosome
• Biological source: Escherichia coli BW25113; More
• Total number of polymer chains: 19
• Total formula weight: 1601760.67

Authors

Paternoga, H.,Beckert, B.,Wilson, D.N. (deposition date: 2023-02-02, release date: 2023-07-19, Last modification date: 2024-04-24)

Primary citation

Paternoga, H.,Crowe-McAuliffe, C.,Bock, L.V.,Koller, T.O.,Morici, M.,Beckert, B.,Myasnikov, A.G.,Grubmuller, H.,Novacek, J.,Wilson, D.N.
Structural conservation of antibiotic interaction with ribosomes.
Nat.Struct.Mol.Biol., 30:1380-1392, 2023

PubMed Abstract: The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.

PubMed: 37550453
DOI: 10.1038/s41594-023-01047-y

Experimental method

ELECTRON MICROSCOPY (2.04 Å)