Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES

Mol Cell. 2015 Feb 5;57(3):422-32. doi: 10.1016/j.molcel.2014.12.016. Epub 2015 Jan 15.

Abstract

The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the CrPV IRES jumpstarts translation in the elongation phase from the ribosomal A site. Here, we present cryoelectron microscopy (cryo-EM) maps of 80S⋅CrPV-STOP ⋅ eRF1 ⋅ eRF3 ⋅ GMPPNP and 80S⋅CrPV-STOP ⋅ eRF1 complexes, revealing a previously unseen binding state of the IRES and directly rationalizing that an eEF2-dependent translocation of the IRES is required to allow the first A-site occupation. During this unusual translocation event, the IRES undergoes a pronounced conformational change to a more stretched conformation. At the same time, our structural analysis provides information about the binding modes of eRF1 ⋅ eRF3 ⋅ GMPPNP and eRF1 in a minimal system. It shows that neither eRF3 nor ABCE1 are required for the active conformation of eRF1 at the intersection between eukaryotic termination and recycling.

Publication types

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

MeSH terms

  • ATP-Binding Cassette Transporters / metabolism
  • Cryoelectron Microscopy / methods
  • Dicistroviridae / chemistry
  • Dicistroviridae / genetics*
  • Eukaryotic Initiation Factors / chemistry
  • Eukaryotic Initiation Factors / metabolism
  • Models, Molecular
  • Molecular Conformation
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptide Termination Factors / chemistry
  • Peptide Termination Factors / metabolism*
  • Protein Biosynthesis
  • RNA, Messenger / chemistry*
  • RNA, Messenger / metabolism
  • RNA, Transfer / chemistry
  • RNA, Transfer / metabolism
  • RNA, Viral / chemistry*
  • RNA, Viral / metabolism
  • Ribosomes / chemistry
  • Ribosomes / metabolism*

Substances

  • ATP-Binding Cassette Transporters
  • Eukaryotic Initiation Factors
  • Peptide Termination Factors
  • RNA, Messenger
  • RNA, Viral
  • RNA, Transfer

Associated data

  • PDB/4D5L
  • PDB/4D5N
  • PDB/4D5Y
  • PDB/4D5Z
  • PDB/4D61
  • PDB/4D66
  • PDB/4D67
  • PDB/4D68