9JQ2

Structure of the Bacterial Ribosome with human tRNA Lys(mcm5h2U34) and mRNA(AAG)

This is a non-PDB format compatible entry.

Summary for 9JQ2

• Entry DOI: 10.2210/pdb9jq2/pdb
• Related: 9JPM 9JPO 9JPP
• EMDB information: 61706 61708 61709 61720
• Descriptor: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (57 entities in total)
• Functional Keywords: trna modifications, decoding, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 55
• Total formula weight: 2212108.36

Authors

Ishiguro, K.,Mo, Y.,Shirouzu, M.,Suzuki, T. (deposition date: 2024-09-27, release date: 2026-03-11, Last modification date: 2026-04-29)

Primary citation

Mo, Y.,Ishiguro, K.,Miyauchi, K.,Sakaguchi, Y.,Hanzawa, Y.,Akiyama, N.,Murayama, A.,Machida, K.,Imataka, H.,Yamashita, A.,Ohira, T.,Shirouzu, M.,Suzuki, T.
Translational regulation by oxidative desulfuration of tRNA modifications.
Nat Commun, 17:-, 2026

PubMed Abstract: Modifications in the anticodon region of transfer RNA (tRNA) are essential for accurate and efficient protein synthesis. 5-Methyl-2-thiouridine derivatives (xmsU) are major modifications at the wobble position of tRNA anticodons decoding purine-ending two-codon sets. Although the thiocarbonyl group of xmsU enhances decoding efficiency, it is chemically susceptible to oxidative desulfuration, yielding 4-pyrimidinone derivatives (xmhU). Here, we identify xmhU derivatives in human cells and mouse tissues and confirm their cellular formation by spike-in experiments. Desulfurized tRNAs carrying 5-methoxycarbonylmethyl-4-pyrimidinone (mcmhU) show impaired codon recognition in a human reconstituted in vitro translation system. The mcmhU modification reduces aminoacylation of tRNAs for lysine, glutamate, and glutamine, but not arginine. Cryogenic electron microscopy reveals the structural basis of altered AAA/AAG decoding by mcmhU at the ribosomal A-site. These findings reveal a mechanism by which oxidative desulfuration of tRNA modifications dynamically regulates codon recognition and protein synthesis under oxidative stress conditions in human and mammalian cells.

PubMed: 41807381
DOI: 10.1038/s41467-026-70126-7

Experimental method

ELECTRON MICROSCOPY (2.61 Å)