9SPI

CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE

This is a non-PDB format compatible entry.

Summary for 9SPI

• Entry DOI: 10.2210/pdb9spi/pdb
• EMDB information: 55091
• Descriptor: tRNA-Ile-AAT-9-1, Large ribosomal subunit protein eL6, Large ribosomal subunit protein uL30, ... (90 entities in total)
• Functional Keywords: cryo-em structure, human, 80s, ribosome, n1-methylpseudouridine
• Biological source: Homo sapiens; More
• Total number of polymer chains: 83
• Total formula weight: 3876757.20

Authors

Rajan, K.S.,Yonath, A. (deposition date: 2025-09-17, release date: 2026-01-21)

Primary citation

Rozman, B.,Broennimann, K.,Rajan, K.S.,Nachshon, A.,Saha, C.,Arazi, T.,Mohan, V.,Geiger, T.,Wollner, C.J.,Richner, J.M.,Westhof, E.,Yonath, A.,Bashan, A.,Stern-Ginossar, N.
N 1 -Methylpseudouridine directly modulates translation dynamics.
Nature, 2026

PubMed Abstract: The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology. A critical feature of this approach is the incorporation of the modified nucleoside N-methylpseudouridine (mΨ), which enhances antigen expression while reducing immunogenicity. However, a comprehensive understanding of how mΨ influences translation remains incomplete. Here we use ribosome profiling at the subcodon resolution to show that mΨ increases ribosome density on synthetic mRNAs, leading to higher protein production independent of innate immune activation or eIF2α phosphorylation. We find that mΨ directly slows ribosome movement in defined sequence contexts while simultaneously promoting translation initiation. Structural studies using cryo-electron microscopy reveal that mΨ alters interactions within the ribosomal decoding centre, providing a mechanistic basis for slowed elongation. Furthermore, by introducing synonymous recoding that disrupts the modification-mediated changes in elongation, we show that the mΨ-dependent enhancement of protein output is modulated by codon composition, and that mΨ impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that mΨ directly modulates translation dynamics, thereby increasing protein yield from synthetic mRNAs in specific sequence contexts.

PubMed: 41535458
DOI: 10.1038/s41586-025-09945-5

Experimental method

ELECTRON MICROSCOPY (2.4 Å)