8G2B
Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAphe, and aminoacylated P-site fMet-tRNAmet at 2.55A resolution
This is a non-PDB format compatible entry.
Summary for 8G2B
| Entry DOI | 10.2210/pdb8g2b/pdb |
| Descriptor | 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (61 entities in total) |
| Functional Keywords | cfr, methyltransferase, multidrug, antibiotic, resistance, methylation, a2503, 23s rrna, 70s ribosome, inhibition of translation, peptidyl transferase center, nascent peptide exit tunnel, iboxamycin, tylosin, ribosome |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 112 |
| Total formula weight | 4569268.90 |
| Authors | Aleksandrova, E.V.,Wu, K.J.Y.,Tresco, B.I.C.,Syroegin, E.A.,Killeavy, E.E.,Balasanyants, S.M.,Svetlov, M.S.,Gregory, S.T.,Atkinson, G.C.,Myers, A.G.,Polikanov, Y.S. (deposition date: 2023-02-03, release date: 2023-12-27, Last modification date: 2024-07-10) |
| Primary citation | Aleksandrova, E.V.,Wu, K.J.Y.,Tresco, B.I.C.,Syroegin, E.A.,Killeavy, E.E.,Balasanyants, S.M.,Svetlov, M.S.,Gregory, S.T.,Atkinson, G.C.,Myers, A.G.,Polikanov, Y.S. Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it. Nat.Chem.Biol., 20:867-876, 2024 Cited by PubMed Abstract: The bacterial ribosome is an essential drug target as many clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent resistance mechanisms to PTC-acting drugs in Gram-positive bacteria is C8-methylation of the universally conserved A2503 nucleobase by Cfr methylase in 23S ribosomal RNA. Despite its clinical importance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. Here, we report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-transfer RNAs. These structures reveal an allosteric rearrangement of nucleotide A2062 upon Cfr-mediated methylation of A2503 that likely contributes to the reduced potency of some PTC inhibitors. Additionally, we provide the structural bases behind two distinct mechanisms of engaging the Cfr-methylated ribosome by the antibiotics iboxamycin and tylosin. PubMed: 38238495DOI: 10.1038/s41589-023-01525-w PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.55 Å) |
Structure validation
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