Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel

Structure. 2018 Mar 6;26(3):437-445.e3. doi: 10.1016/j.str.2018.01.013. Epub 2018 Feb 15.

Abstract

Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation.

Keywords: RNA structure; cryo-EM; protein synthesis; ribosome; stem loop; translational control.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Cryoelectron Microscopy
  • Escherichia coli / genetics*
  • Models, Molecular
  • Molecular Conformation
  • Protein Biosynthesis
  • Protein Domains
  • RNA, Bacterial / chemistry
  • RNA, Messenger / chemistry*
  • RNA, Messenger / metabolism*
  • RNA, Transfer / chemistry*
  • RNA, Transfer / metabolism*
  • Ribosomes / chemistry

Substances

  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Transfer