5UYP

70S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc)

This is a non-PDB format compatible entry.

Summary for 5UYP

• Entry DOI: 10.2210/pdb5uyp/pdb
• Related: 5UYK 5UYL 5UYM 5UYN 5UYQ
• EMDB information: 8615 8616 8617 8618 8619 8620
• Descriptor: 50S ribosomal protein L2, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (62 entities in total)
• Functional Keywords: ribosome, ef-tu, trna
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 60
• Total formula weight: 2288800.94

Authors

Loveland, A.B.,Demo, G.,Grigorieff, N.,Korostelev, A.A. (deposition date: 2017-02-24, release date: 2017-06-07, Last modification date: 2024-03-13)

Primary citation

Loveland, A.B.,Demo, G.,Grigorieff, N.,Korostelev, A.A.
Ensemble cryo-EM elucidates the mechanism of translation fidelity
Nature, 546:113-117, 2017

PubMed Abstract: Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit. A transient conformation of decoding-centre nucleotide G530 stabilizes the cognate codon-anticodon helix, initiating step-wise 'latching' of the decoding centre. The resulting closure of the 30S subunit docks EF-Tu at the sarcin-ricin loop of the 50S subunit, activating EF-Tu for GTP hydrolysis and enabling accommodation of the aminoacyl-tRNA. By contrast, near-cognate complexes fail to induce the G530 latch, thus favouring open 30S pre-accommodation intermediates with inactive EF-Tu. This work reveals long-sought structural differences between the pre-accommodation of cognate and near-cognate tRNAs that elucidate the mechanism of accurate decoding.

PubMed: 28538735
DOI: 10.1038/nature22397

Experimental method

ELECTRON MICROSCOPY (3.9 Å)