12DP

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with sparsomycin, mRNA, and aminoacylated initiator P-site fMet-tRNAmet at 2.95A resolution

This is a non-PDB format compatible entry.

Summary for 12DP

• Entry DOI: 10.2210/pdb12dp/pdb
• Descriptor: 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (61 entities in total)
• Functional Keywords: sparsomycin; antibiotic; ribosome; translation; inhibition; structure; peptidyl transferase center; nascent peptide exit tunnel; aminoacyl-trna; peptidyl-trna; initiator trna; context-specificity of drug action; itp-seq, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 108
• Total formula weight: 4470839.53

Authors

Paranjpe, M.N.,Leroy, E.C.,Syroegin, E.A.,Flemmich, L.,Thaler, J.,Gillard, M.,Bougas, A.,Kournoutou, G.,Dinos, G.P.,Renault, T.T.,Micura, R.,Innis, C.A.,Polikanov, Y.S. (deposition date: 2026-03-30, release date: 2026-09-09)

Primary citation

Paranjpe, M.N.,Leroy, E.C.,Syroegin, E.A.,Flemmich, L.,Thaler, J.,Gillard, M.,Bougas, A.,Kournoutou, G.,Dinos, G.P.,Renault, T.T.,Micura, R.,Innis, C.A.,Polikanov, Y.S.
Sparsomycin inhibits translation through a conserved mechanism across all domains of life.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been known to target the ribosomal peptidyl transferase center (PTC), previous structural studies suggested that SPA binds differently to bacterial ribosomes compared to their archaeal and eukaryotic counterparts-an unexpected conclusion given the high evolutionary conservation of the ribosomal catalytic center. Here, we show that SPA inhibits a majority of elongation-competent bacterial ribosomal complexes and present X-ray crystal structures of Thermus thermophilus 70S ribosomes stalled by SPA at the initiation and early elongation stages of translation. These structures reveal that SPA binds to the bacterial ribosome in a manner essentially identical to that observed in archaeal and eukaryotic ribosomes, establishing a unified structural mechanism of SPA action across all domains of life. In this conserved binding mode, SPA occupies the A-site cleft of the PTC and forms an extensive network of interactions with universally conserved ribosomal RNA nucleotides and the CCA-end of the P-site transfer RNA (tRNA), thereby stabilizing the peptidyl-tRNA substrate while sterically blocking accommodation of an incoming aminoacyl-tRNA. By clarifying the mode of action of SPA on the bacterial ribosome, our work provides a structural framework for the rational design of SPA derivatives with improved potency and bacterial specificity.

PubMed: 42581761
DOI: 10.1093/nar/gkag761

Experimental method

X-RAY DIFFRACTION (2.95 Å)