Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes

Nucleic Acids Res. 2019 Sep 5;47(15):8282-8300. doi: 10.1093/nar/gkz570.


eIF3 is a large multiprotein complex serving as an essential scaffold promoting binding of other eIFs to the 40S subunit, where it coordinates their actions during translation initiation. Perhaps due to a high degree of flexibility of multiple eIF3 subunits, a high-resolution structure of free eIF3 from any organism has never been solved. Employing genetics and biochemistry, we previously built a 2D interaction map of all five yeast eIF3 subunits. Here we further improved the previously reported in vitro reconstitution protocol of yeast eIF3, which we cross-linked and trypsin-digested to determine its overall shape in 3D by advanced mass-spectrometry. The obtained cross-links support our 2D subunit interaction map and reveal that eIF3 is tightly packed with its WD40 and RRM domains exposed. This contrasts with reported cryo-EM structures depicting eIF3 as a molecular embracer of the 40S subunit. Since the binding of eIF1 and eIF5 further fortified the compact architecture of eIF3, we suggest that its initial contact with the 40S solvent-exposed side makes eIF3 to open up and wrap around the 40S head with its extended arms. In addition, we mapped the position of eIF5 to the region below the P- and E-sites of the 40S subunit.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / genetics
  • Cryoelectron Microscopy
  • Eukaryotic Initiation Factor-1 / chemistry*
  • Eukaryotic Initiation Factor-1 / genetics
  • Eukaryotic Initiation Factor-1 / metabolism
  • Eukaryotic Initiation Factor-3 / chemistry*
  • Eukaryotic Initiation Factor-3 / genetics
  • Eukaryotic Initiation Factor-3 / metabolism
  • Eukaryotic Initiation Factor-5 / chemistry*
  • Eukaryotic Initiation Factor-5 / genetics
  • Eukaryotic Initiation Factor-5 / metabolism
  • Models, Molecular
  • Peptide Chain Initiation, Translational*
  • Protein Binding
  • Protein Domains
  • Ribosome Subunits, Small, Eukaryotic / genetics
  • Ribosome Subunits, Small, Eukaryotic / metabolism*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae / ultrastructure
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism


  • Eukaryotic Initiation Factor-1
  • Eukaryotic Initiation Factor-3
  • Eukaryotic Initiation Factor-5
  • Saccharomyces cerevisiae Proteins