7OSM

Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands

This is a non-PDB format compatible entry.

Summary for 7OSM

• Entry DOI: 10.2210/pdb7osm/pdb
• Related: 7OSA
• Descriptor: 25S rRNA, 60S ribosomal protein L7-A, 60S ribosomal protein L8-A, ... (86 entities in total)
• Functional Keywords: translocation, eef2, trna, mrna, eukaryotic ribosome, ribosome
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 83
• Total formula weight: 3300084.67

Authors

Djumagulov, M.,Jenner, L.,Rozov, A.,Demeshkina, N.,Yusupov, M.,Yusupova, G. (deposition date: 2021-06-09, release date: 2021-12-08, Last modification date: 2024-01-31)

Primary citation

Djumagulov, M.,Demeshkina, N.,Jenner, L.,Rozov, A.,Yusupov, M.,Yusupova, G.
Accuracy mechanism of eukaryotic ribosome translocation.
Nature, 600:543-546, 2021

PubMed Abstract: Translation of the genetic code into proteins is realized through repetitions of synchronous translocation of messenger RNA (mRNA) and transfer RNAs (tRNA) through the ribosome. In eukaryotes translocation is ensured by elongation factor 2 (eEF2), which catalyses the process and actively contributes to its accuracy. Although numerous studies point to critical roles for both the conserved eukaryotic posttranslational modification diphthamide in eEF2 and tRNA modifications in supporting the accuracy of translocation, detailed molecular mechanisms describing their specific functions are poorly understood. Here we report a high-resolution X-ray structure of the eukaryotic 80S ribosome in a translocation-intermediate state containing mRNA, naturally modified eEF2 and tRNAs. The crystal structure reveals a network of stabilization of codon-anticodon interactions involving diphthamide and the hypermodified nucleoside wybutosine at position 37 of phenylalanine tRNA, which is also known to enhance translation accuracy. The model demonstrates how the decoding centre releases a codon-anticodon duplex, allowing its movement on the ribosome, and emphasizes the function of eEF2 as a 'pawl' defining the directionality of translocation. This model suggests how eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs undergo large-scale molecular reorganizations to ensure maintenance of the mRNA reading frame during the complex process of translocation.

PubMed: 34853469
DOI: 10.1038/s41586-021-04131-9

Experimental method

X-RAY DIFFRACTION (3 Å)