Position of Eukaryotic Initiation Factor eIF5B on the 80S Ribosome Mapped by Directed Hydroxyl Radical Probing

EMBO J. 2007 Jul 11;26(13):3109-23. doi: 10.1038/sj.emboj.7601751. Epub 2007 Jun 14.


Eukaryotic translation initiation factor eIF5B is a ribosome-dependent GTPase that mediates displacement of initiation factors from the 40S ribosomal subunit in 48S initiation complexes and joining of 40S and 60S subunits. Here, we determined eIF5B's position on 80S ribosomes by directed hydroxyl radical cleavage. In the resulting model, eIF5B is located in the intersubunit cleft of the 80S ribosome: domain 1 is positioned near the GTPase activating center of the 60S subunit, domain 2 interacts with the 40S subunit (helices 3, 5 and the base of helix 15 of 18S rRNA and ribosomal protein (rp) rpS23), domain 3 is sandwiched between subunits and directly contacts several ribosomal elements including Helix 95 of 28S rRNA and helix 44 of 18S rRNA, domain 4 is near the peptidyl-transferase center and its helical subdomain contacts rpL10E. The cleavage data also indicate that binding of eIF5B might induce conformational changes in both subunits, with ribosomal segments wrapping around the factor. Some of these changes could also occur upon binding of other translational GTPases, and may contribute to factor recognition.

MeSH terms

  • Base Sequence
  • Cysteine / genetics
  • Cysteine / metabolism
  • Eukaryotic Initiation Factors / chemistry*
  • Eukaryotic Initiation Factors / genetics
  • Eukaryotic Initiation Factors / isolation & purification
  • Eukaryotic Initiation Factors / metabolism*
  • Humans
  • Hydroxyl Radical / metabolism*
  • Models, Molecular
  • Mutation / genetics
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Protein Subunits / chemistry
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / genetics
  • Ribosomes / metabolism*


  • Eukaryotic Initiation Factors
  • Protein Subunits
  • RNA, Ribosomal
  • eukaryotic initiation factor-5B
  • Hydroxyl Radical
  • Cysteine