8YLR

State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation

This is a non-PDB format compatible entry.

Summary for 8YLR

• Entry DOI: 10.2210/pdb8ylr/pdb
• EMDB information: 38668
• Descriptor: 18S rRNA, Large ribosomal subunit protein eL8A, Large ribosomal subunit protein uL6A, ... (81 entities in total)
• Functional Keywords: 80s, eef3, eef2, ribosome
• Biological source: Saccharomyces cerevisiae S288C; More
• Total number of polymer chains: 82
• Total formula weight: 3284771.43

Authors

Cheng, J.,Wu, C.L.,Li, J.X.,Zhang, X.Z. (deposition date: 2024-03-06, release date: 2024-12-11, Last modification date: 2025-07-02)

Primary citation

Cheng, J.,Wu, C.,Li, J.,Yang, Q.,Zhao, M.,Zhang, X.
Capturing eukaryotic ribosome dynamics in situ at high resolution.
Nat.Struct.Mol.Biol., 32:698-708, 2025

PubMed Abstract: Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis. Over 20 distinct conformations were identified by three-dimensional classification with resolutions typically higher than 4 Å. These conformations were used to reconstruct a complete elongation cycle of eukaryotic translation with elongation factors (eEFs). We found that compact eEF2 anchors to the partially rotated ribosome after subunit rolling and hypothesize that it stabilizes the local conformation for peptidyl transfer. Moreover, open-eEF3 binding to a fully rotated ribosome was observed, whose conformational change was coupled with head swiveling and body back-rotation of the 40S subunit.

PubMed: 39789210
DOI: 10.1038/s41594-024-01454-9

Experimental method

ELECTRON MICROSCOPY (3.9 Å)