9d0i

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Se-cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.45A resolution

spinqualitylabelsall models 9d0i, resolution 2.45Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9d0i is a 20 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.45Å Ligands: 0TD, 2MA, 2MG, 31H, 4OC, 4SU, 5MC, 5MU, A1A1K, G7M, K, M2G, MA6, MG, MIA, OMC, OMG, OMU, PSU, UR3, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RL2_THET8 One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B] Publication Abstract from PubMed We recently reported the conception and synthesis of cresomycin (CRM), a fully synthetic lincosamide antibiotic effective in vitro and in vivo against multidrug-resistant Gram-positive and Gram-negative bacteria. In this work, we describe the chemical synthesis and characterization of CRM sulfur atom replacement analogs C-CRM (S --> CH(2)), O-CRM (S --> O), and Se-CRM (S --> Se). Comparison of high-resolution co-crystal structures showed that the four analogs adopted identical conformations when bound to the bacterial ribosome, but due to variations of </=1 A in the bond lengths between the anomeric carbon and the varied atoms, only the S and Se heteroatoms of CRM and Se-CRM, respectively, were positioned to interact with the pi-face of nucleobase G2505. C-CRM and O-CRM did not benefit from such stabilizations, with correspondingly negative consequences in both target engagement and antibacterial activities. We therefore conclude that the sulfur atom of the lincosamides is important in ribosomal binding. Why Sulfur is Important in Lincosamide Antibiotics.,Wu KJY, Aleksandrova EV, Robinson PJ, Benedetto AE, Yu M, Tresco BIC, See DNY, Jiang T, Ramkissoon A, Dunand CF, Svetlov MS, Lee J, Polikanov YS, Myers AG Chem. 2025 Jul 10;11(7):102480. doi: 10.1016/j.chempr.2025.102480. Epub 2025 Mar , 7. PMID:40787583 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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