EMD-28643

Single-particle
2.45 Å
EMD-28643 Deposition: 22/10/2022
Map released: 06/09/2023
Last modified: 06/09/2023
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-28643

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

EMD-28643

Single-particle
2.45 Å
EMD-28643 Deposition: 22/10/2022
Map released: 06/09/2023
Last modified: 06/09/2023
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Saccharomyces cerevisiae, Taura syndrome virus
Sample: Hypopseudouridylated ribosome with TSV IRES, eEF2 and GDP
Fitted models: 8ewc (Avg. Q-score: 0.532)
Raw data: EMPIAR-12070

Deposition Authors: Zhao Y , Rai J , Li H
Regulation of translation by ribosomal RNA pseudouridylation.
Zhao Y , Rai J , Li H
(2023) Sci Adv , 9 , eadg8190 - eadg8190
PUBMED: 37595043
DOI: doi:10.1126/sciadv.adg8190
ISSN: 2375-2548
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.