Structure of the ribosome-bound cricket paralysis virus IRES RNA

Nat Struct Mol Biol. 2006 Dec;13(12):1092-6. doi: 10.1038/nsmb1177. Epub 2006 Nov 19.

Abstract

Internal ribosome entry sites (IRESs) facilitate an alternative, end-independent pathway of translation initiation. A particular family of dicistroviral IRESs can assemble elongation-competent 80S ribosomal complexes in the absence of canonical initiation factors and initiator transfer RNA. We present here a cryo-EM reconstruction of a dicistroviral IRES bound to the 80S ribosome. The resolution of the cryo-EM reconstruction, in the subnanometer range, allowed the molecular structure of the complete IRES in its active, ribosome-bound state to be solved. The structure, harboring three pseudoknot-containing domains, each with a specific functional role, shows how defined elements of the IRES emerge from a compactly folded core and interact with the key ribosomal components that form the A, P and E sites, where tRNAs normally bind. Our results exemplify the molecular strategy for recruitment of an IRES and reveal the dynamic features necessary for internal initiation.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Cryoelectron Microscopy
  • Gryllidae / virology*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Paralysis
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA Viruses / genetics*
  • RNA, Viral / chemistry*
  • RNA, Viral / metabolism*
  • RNA, Viral / ultrastructure
  • Ribosomal Proteins / chemistry
  • Ribosomal Proteins / metabolism
  • Ribosomes / chemistry*
  • Ribosomes / metabolism*
  • Ribosomes / ultrastructure
  • Saccharomyces cerevisiae / chemistry
  • Saccharomyces cerevisiae / metabolism
  • Structural Homology, Protein

Substances

  • RNA, Viral
  • Ribosomal Proteins
  • ribosomal protein S80

Associated data

  • PDB/2NOQ