8EVP

Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I

This is a non-PDB format compatible entry.

Summary for 8EVP

• Entry DOI: 10.2210/pdb8evp/pdb
• EMDB information: 28632
• Descriptor: 40S ribosomal protein S0-A, 40S ribosomal protein S13, 40S ribosomal protein S14-A, ... (82 entities in total)
• Functional Keywords: rrna pseudouridylation, ires initiation, confomation, eef2, ribosome
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 80
• Total formula weight: 3191236.17

Authors

Zhao, Y.,Rai, J.,Li, H. (deposition date: 2022-10-20, release date: 2023-09-06)

Primary citation

Zhao, Y.,Rai, J.,Li, H.
Regulation of translation by ribosomal RNA pseudouridylation.
Sci Adv, 9:eadg8190-eadg8190, 2023

PubMed Abstract: Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.

PubMed: 37595043
DOI: 10.1126/sciadv.adg8190

Experimental method

ELECTRON MICROSCOPY (2.38 Å)