Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes

EMBO J. 2008 Jun 4;27(11):1609-21. doi: 10.1038/emboj.2008.90. Epub 2008 May 8.


The position of mRNA on 40S ribosomal subunits in eukaryotic initiation complexes was determined by UV crosslinking using mRNAs containing uniquely positioned 4-thiouridines. Crosslinking of mRNA positions (+)11 to ribosomal protein (rp) rpS2(S5p) and rpS3(S3p), and (+)9-(+)11 and (+)8-(+)9 to h18 and h34 of 18S rRNA, respectively, indicated that mRNA enters the mRNA-binding channel through the same layers of rRNA and proteins as in prokaryotes. Upstream of the P-site, the proximity of positions (-)3/(-)4 to rpS5(S7p) and h23b, (-)6/(-)7 to rpS14(S11p), and (-)8-(-)11 to the 3'-terminus of 18S rRNA (mRNA/rRNA elements forming the bacterial Shine-Dalgarno duplex) also resembles elements of the bacterial mRNA path. In addition to these striking parallels, differences between mRNA paths included the proximity in eukaryotic initiation complexes of positions (+)7/(+)8 to the central region of h28, (+)4/(+)5 to rpS15(S19p), and (-)6 and (-)7/(-)10 to eukaryote-specific rpS26 and rpS28, respectively. Moreover, we previously determined that eukaryotic initiation factor2alpha (eIF2alpha) contacts position (-)3, and now report that eIF3 interacts with positions (-)8-(-)17, forming an extension of the mRNA-binding channel that likely contributes to unique aspects of eukaryotic initiation.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Eukaryotic Initiation Factor-3 / chemistry
  • Eukaryotic Initiation Factor-3 / metabolism*
  • Eukaryotic Initiation Factor-3 / radiation effects
  • Humans
  • Mice
  • Peptide Chain Initiation, Translational*
  • Protein Conformation
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism*
  • RNA, Messenger / radiation effects
  • Ribosomal Proteins / chemistry
  • Ribosomal Proteins / metabolism*
  • Ribosomal Proteins / radiation effects
  • Ribosomes / chemistry
  • Ribosomes / metabolism*
  • Ribosomes / radiation effects
  • Thiouridine / chemistry
  • Ultraviolet Rays


  • Eukaryotic Initiation Factor-3
  • RNA, Messenger
  • Ribosomal Proteins
  • Thiouridine