Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation

Nucleic Acids Res. 2013 Aug;41(15):7512-21. doi: 10.1093/nar/gkt510. Epub 2013 Jun 13.


The initiation of protein synthesis plays an essential regulatory role in human biology. At the center of the initiation pathway, the 13-subunit eukaryotic translation initiation factor 3 (eIF3) controls access of other initiation factors and mRNA to the ribosome by unknown mechanisms. Using electron microscopy (EM), bioinformatics and biochemical experiments, we identify two highly conserved RNA-binding motifs in eIF3 that direct translation initiation from the hepatitis C virus internal ribosome entry site (HCV IRES) RNA. Mutations in the RNA-binding motif of subunit eIF3a weaken eIF3 binding to the HCV IRES and the 40S ribosomal subunit, thereby suppressing eIF2-dependent recognition of the start codon. Mutations in the eIF3c RNA-binding motif also reduce 40S ribosomal subunit binding to eIF3, and inhibit eIF5B-dependent steps downstream of start codon recognition. These results provide the first connection between the structure of the central translation initiation factor eIF3 and recognition of the HCV genomic RNA start codon, molecular interactions that likely extend to the human transcriptome.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Codon, Initiator / genetics
  • Codon, Initiator / metabolism
  • Eukaryotic Initiation Factor-3 / genetics
  • Eukaryotic Initiation Factor-3 / metabolism*
  • Helix-Loop-Helix Motifs
  • Hepacivirus / genetics
  • Hepacivirus / metabolism*
  • Humans
  • Multiprotein Complexes / genetics
  • Multiprotein Complexes / metabolism
  • Mutation
  • Protein Binding
  • Protein Biosynthesis*
  • Protein Interaction Mapping
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • Ribosome Subunits, Small, Eukaryotic / genetics
  • Ribosome Subunits, Small, Eukaryotic / metabolism
  • Ribosomes / genetics
  • Ribosomes / metabolism


  • Codon, Initiator
  • EIF3A protein, human
  • Eukaryotic Initiation Factor-3
  • Multiprotein Complexes
  • RNA, Viral