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A new understanding of the decoding principle on the ribosome


During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon–anticodon interactions in the decoding centre1,2,3,4,5,6,7,8,9. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon2,3,10,11,12,13,14. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site15,16,17, actively monitor cognate tRNA18, and that recognition of the correct codon–anticodon duplex induces an overall ribosome conformational change (domain closure)19. Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1–3.4 Å resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson–Crick base pairs. When U·G and G·U mismatches, generally considered to form wobble base pairs, are at the first or second codon–anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C·G pair. This by itself, or with distortions in the codon–anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.

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Figure 1: Codon–anticodon interactions in the decoding centre on the 70S ribosome.
Figure 2: The nature of the decoding centre.
Figure 3: The principle of decoding.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates and structure factors for the determined crystal structures are deposited in the Protein Data Bank under accession numbers 3TVF and 3TVE (cognate tRNA2 Leu complex), 3UYE and 3UYD (near-cognate tRNA2 Leu complex), 3UZ3 and3UZ1 (near-cognate tRNA2 Leu complex with paromomycin),3UZ6 and 3UZ9 (cognate tRNATyr complex), 3UZG and 3UZF (near-cognate tRNATyr complex), and 3UZL and 3UZK (near-cognate tRNATyr complex with paromomycin).


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We are grateful to C. Schulze-Briese and the staff at the Swiss Light Source (Switzerland) for help during synchrotron X-ray data collection. We thank S. Duclaud for ribosome preparation and the staff of the Structural Biology Department core facility at Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg. This work was supported by ANR BLAN07-3_190451 (to M.Y.), ANR-07-PCVI-0015-01 (to G.Y.), Fondation pour la Recherche Médicale en France (to N.D.) and by the European Commission SPINE2.

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Authors and Affiliations



N.D. and L.J. conducted experiments and performed analysis. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Marat Yusupov or Gulnara Yusupova.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-11, Supplementary Tables 1-3 and additional references. (PDF 5357 kb)

Supplementary Movie 1

This file contains an animation showing deformation of the codon-anticodon mini-helix and the A site tRNA anticodon loop upon transition from cognate to near-cognate states. The models are colored as follows: the mRNA codon is in yellow and the tRNA anticodon loop is in red. See the main text and Fig. 2d. (MOV 89 kb)

Supplementary Movie 2

This file contains an animation showing changes in the decoding pocket and its environment upon binding of aminoglycoside antibiotic paromomycin (PAR). The comparison is shown for the tRNATyr near-cognate state. The color code is the following: near-cognate tRNATyr, - red; mRNA, - yellow; PAR, - green; ‘530’ loop and helix 44 of 16S rRNA, - aquamarine; helix 69 of 23S rRNA, - grey. Refer to the main text and Fig. 2e. (MOV 164 kb)

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Demeshkina, N., Jenner, L., Westhof, E. et al. A new understanding of the decoding principle on the ribosome. Nature 484, 256–259 (2012).

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