9YPZ

Vacant ribosome with P-site tRNA, substate 1, Structure Ia

This is a non-PDB format compatible entry.

Summary for 9YPZ

• Entry DOI: 10.2210/pdb9ypz/pdb
• EMDB information: 73315
• Descriptor: 28S ribosomal RNA, 60S ribosomal protein L7a, 60S ribosomal protein L9, ... (85 entities in total)
• Functional Keywords: gtpbp1, trna, gcp, complex, ribosome
• Biological source: Oryctolagus cuniculus (rabbit); More
• Total number of polymer chains: 82
• Total formula weight: 3437724.89

Authors

Susorov, D.,Korostelev, A.A. (deposition date: 2025-10-14, release date: 2025-12-24)

Primary citation

Susorov, D.,Miscicka, A.,Golovenko, D.,Loveland, A.B.,Zinoviev, A.,Pestova, T.V.,Korostelev, A.A.
Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1.
Nat Commun, 2025

PubMed Abstract: GTP-binding protein 1 (GTPBP1) is a widespread translational GTPase closely related to elongation factor eEF1A. The loss of GTPBP1 leads to neurodevelopmental and neurodegenerative disorders in animals. Although linked to translation and quality control mechanisms, GTPBP1 molecular functions remain largely obscure. Similarly to eEF1A, GTPBP1 delivers aminoacyl-tRNA to the ribosome, but the ensuing GTPBP1-mediated elongation is slow. Here, using cryo-EM of mammalian 80S ribosomal complexes bound to GTPBP1 and aa-tRNA with GTP or the non-hydrolysable analog GDPCP, we show that the distinct GTPBP1 architecture and interactions with tRNA underlie slow GTPBP1 dissociation after GTP hydrolysis, resulting in delayed tRNA accommodation. Slow dissociation correlates with an extended proofreading stage and higher accuracy of GTPBP1-mediated decoding, potentially allowing GTPBP1 to elicit its putative quality control functions. GTPBP1 visualization provides the foundation for mapping and elucidating GTPBP1 mutations associated with human diseases.

PubMed: 41350250
DOI: 10.1038/s41467-025-66833-2

Experimental method

ELECTRON MICROSCOPY (2.9 Å)