8CGI
Pentacycline TP038 bound to the 30S head
Summary for 8CGI
| Entry DOI | 10.2210/pdb8cgi/pdb |
| Related | 8CA7 8CAI 8CAM 8CAZ 8CEP 8CEU 8CF1 8CF8 8CGD |
| EMDB information | 16520 16526 16530 16536 16612 16613 16615 16620 16641 16644 |
| Descriptor | Large ribosomal subunit protein bL31A, Pentacycline, POTASSIUM ION, ... (13 entities in total) |
| Functional Keywords | antibiotic, ribosome |
| Biological source | Escherichia coli BW25113 More |
| Total number of polymer chains | 9 |
| Total formula weight | 616724.08 |
| Authors | Paternoga, H.,Crowe-McAuliffe, C.,Novacek, J.,Wilson, D.N. (deposition date: 2023-02-04, release date: 2023-07-26, 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 Cited by 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: 37550453DOI: 10.1038/s41594-023-01047-y PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (1.89 Å) |
Structure validation
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