9PN5

Composite map of hypomethylated 80S ribosome treated with hygromycin B

This is a non-PDB format compatible entry.

Summary for 9PN5

• Entry DOI: 10.2210/pdb9pn5/pdb
• EMDB information: 71745
• Descriptor: Small ribosomal subunit protein uS2A, Small ribosomal subunit protein uS15, Small ribosomal subunit protein uS11A, ... (82 entities in total)
• Functional Keywords: 2'-o-methylation, ribosome, rrna modification
• Biological source: Saccharomyces cerevisiae BY4741; More
• Total number of polymer chains: 78
• Total formula weight: 3043226.92

Authors

Zhao, Y.,Li, H. (deposition date: 2025-07-19, release date: 2026-05-20)

Primary citation

Zhao, Y.,Rai, J.,Cohen, L.N.,Shu, Y.,Xu, C.,Goswami, H.,Chen, X.,Jin, H.,Marchand, V.,Motorin, Y.,Ghalei, H.,Li, H.
2'-O-Methylation maintains ribosome structural and translation integrity.
Mol.Cell, 86:1495-1510.e7, 2026

PubMed Abstract: In eukaryotic ribosomes, ∼2% of RNA nucleotides undergo 2'-O-methylation, a conserved cellular mechanism thought to be critical for maintaining and regulating translation. Here, we use ribosome profiling, translation assays, proteomics, and high-resolution structural analyses to show that loss of native 2'-O-methylation in yeast ribosomes disproportionally affects the translation of ribosomal protein transcripts, driven by changes in codon usage and recognition of structured RNA. Translation reprogramming by the hypomethylated ribosomes is supported by reduced thermostability and high-resolution evidence of altered ribosomal structures and conformations. Consistent with the roles of the affected proteins in sustaining cellular fitness, hypomethylated ribosomes under stress exhibit a selective loss of downregulated proteins and misassembly associated with methylation loss. Our data provide structural and mechanistic insights into how 2'-O-methylation supports ribosome integrity and mediates cellular stress responses.

PubMed: 41928510
DOI: 10.1016/j.molcel.2026.03.008

Experimental method

ELECTRON MICROSCOPY (1.75 Å)