4V4B

Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.

This is a non-PDB format compatible entry.

Summary for 4V4B

• Entry DOI: 10.2210/pdb4v4b/pdb
• Related: 1FFK 1FJF 1FKA 1GIX 1GIY 1K5X 1K5Y 1MMS 1MZP 1NOU
• EMDB information: 1067
• Descriptor: 18S ribosomal RNA, 40S ribosomal protein S20, 40S ribosomal protein S14-A, ... (47 entities in total)
• Functional Keywords: 80s ribosome, 40s ribosomal subunit, eef2, trna translocation, sordarin, cryo-em, ribosome
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 47
• Total formula weight: 2305214.93

Authors

Spahn, C.M.,Gomez-Lorenzo, M.G.,Grassucci, R.A.,Jorgensen, R.,Andersen, G.R.,Beckmann, R.,Penczek, P.A.,Ballesta, J.P.G.,Frank, J. (deposition date: 2004-01-06, release date: 2014-07-09, Last modification date: 2024-02-28)

Primary citation

Spahn, C.M.,Gomez-Lorenzo, M.G.,Grassucci, R.A.,Jorgensen, R.,Andersen, G.R.,Beckmann, R.,Penczek, P.A.,Ballesta, J.P.,Frank, J.
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Embo J., 23:1008-1019, 2004

PubMed Abstract: An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.

PubMed: 14976550
DOI: 10.1038/sj.emboj.7600102

Experimental method

ELECTRON MICROSCOPY (11.7 Å)