5JUP

Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit)

This is a non-PDB format compatible entry.

Summary for 5JUP

• Entry DOI: 10.2210/pdb5jup/pdb
• Related: 5JUO 5JUS 5JUT 5JUU
• EMDB information: 6643 6644 6645 6646 6647 6648 6649 6650 6652 6653
• Descriptor: 18S ribosomal RNA, eL6 (yeast L6), uL30 (yeast L7), ... (86 entities in total)
• Functional Keywords: 80s-ires, eef2, translocation, sordarin, ribosome
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 83
• Total formula weight: 3340490.76

Authors

Abeyrathne, P.,Koh, C.S.,Grant, T.,Grigorieff, N.,Korostelev, A.A. (deposition date: 2016-05-10, release date: 2016-10-05, Last modification date: 2019-11-27)

Primary citation

Abeyrathne, P.D.,Koh, C.S.,Grant, T.,Grigorieff, N.,Korostelev, A.A.
Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
Elife, 5:-, 2016

PubMed Abstract: Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation.

PubMed: 27159452
DOI: 10.7554/eLife.14874

Experimental method

ELECTRON MICROSCOPY (3.5 Å)