5IB7

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin

This is a non-PDB format compatible entry.

Summary for 5IB7

• Entry DOI: 10.2210/pdb5ib7/pdb
• Descriptor: 16S ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (62 entities in total)
• Functional Keywords: translation, ribosome, mismatch
• Biological source: Thermus thermophilus HB8; More
• Total number of polymer chains: 109
• Total formula weight: 4540509.36

Authors

Rozov, A.,Demeshkina, N.,Yusupov, M.,Yusupova, G. (deposition date: 2016-02-22, release date: 2016-05-25, Last modification date: 2024-01-10)

Primary citation

Rozov, A.,Westhof, E.,Yusupov, M.,Yusupova, G.
The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.
Nucleic Acids Res., 44:6434-6441, 2016

PubMed Abstract: Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G•C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.

PubMed: 27174928
DOI: 10.1093/nar/gkw431

Experimental method

X-RAY DIFFRACTION (2.99 Å)