8BHJ

Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and Am6AA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site

This is a non-PDB format compatible entry.

Summary for 8BHJ

• Entry DOI: 10.2210/pdb8bhj/pdb
• Related: 8BF7 8BGE 8BGH 8BH4
• EMDB information: 16015 16029 16031 16047 16057
• Descriptor: 50S ribosomal protein L2, 50S ribosomal protein L16, 50S ribosomal protein L17, ... (55 entities in total)
• Functional Keywords: m6a, mrna modification, trna recognition, translation
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 55
• Total formula weight: 2191150.14

Authors

Koziej, L.,Glatt, S. (deposition date: 2022-10-31, release date: 2023-08-16, Last modification date: 2024-10-16)

Primary citation

Jain, S.,Koziej, L.,Poulis, P.,Kaczmarczyk, I.,Gaik, M.,Rawski, M.,Ranjan, N.,Glatt, S.,Rodnina, M.V.
Modulation of translational decoding by m 6 A modification of mRNA.
Nat Commun, 14:4784-4784, 2023

PubMed Abstract: N-methyladenosine (mA) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. mA in the mRNA coding regions inhibits translation elongation. Here, we show how mA modulates decoding in the bacterial translation system using a combination of rapid kinetics, smFRET and single-particle cryo-EM. We show that, while the modification does not impair the initial binding of aminoacyl-tRNA to the ribosome, in the presence of mA fewer ribosomes complete the decoding process due to the lower stability of the complexes and enhanced tRNA drop-off. The mRNA codon adopts a π-stacked codon conformation that is remodeled upon aminoacyl-tRNA binding. mA does not exclude canonical codon-anticodon geometry, but favors alternative more dynamic conformations that are rejected by the ribosome. These results highlight how modifications outside the Watson-Crick edge can still interfere with codon-anticodon base pairing and complex recognition by the ribosome, thereby modulating the translational efficiency of modified mRNAs.

PubMed: 37553384
DOI: 10.1038/s41467-023-40422-7

Experimental method

ELECTRON MICROSCOPY (2.81 Å)