8FZH

Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State II-D)

This is a non-PDB format compatible entry.

Summary for 8FZH

• Entry DOI: 10.2210/pdb8fzh/pdb
• EMDB information: 29628
• Descriptor: 16S Ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (60 entities in total)
• Functional Keywords: release factor 1, termination complex, cryo-em, trna, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 58
• Total formula weight: 2281488.85

Authors

Rybak, M.Y.,Li, L.,Lin, J.,Gagnon, M.G. (deposition date: 2023-01-28, release date: 2024-07-17, Last modification date: 2025-03-19)

Primary citation

Li, L.,Rybak, M.Y.,Lin, J.,Gagnon, M.G.
The ribosome termination complex remodels release factor RF3 and ejects GDP.
Nat.Struct.Mol.Biol., 31:1909-1920, 2024

PubMed Abstract: Translation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then exchange GDP for GTP. The 70S ribosome termination complex (70S-TC) accelerates GDP exchange in RF3, suggesting that the 70S-TC can function as the guanine nucleotide exchange factor for RF3. Here, we use cryogenic-electron microscopy to elucidate the mechanism of GDP dissociation from RF3 catalyzed by the Escherichia coli 70S-TC. The non-rotated ribosome bound to RF1 remodels RF3 and induces a peptide flip in the phosphate-binding loop, efficiently ejecting GDP. Binding of GTP allows RF3 to dock at the GTPase center, promoting the dissociation of RF1 from the ribosome. The structures recapitulate the functional cycle of RF3 on the ribosome and uncover the mechanism by which the 70S-TC allosterically dismantles the phosphate-binding groove in RF3, a previously overlooked function of the ribosome.

PubMed: 39030416
DOI: 10.1038/s41594-024-01360-0

Experimental method

ELECTRON MICROSCOPY (2.9 Å)