eIF3j is located in the decoding center of the human 40S ribosomal subunit

Protein synthesis in all cells begins with the ordered binding of the small ribosomal subunit to messenger RNA (mRNA) and transfer RNA (tRNA). In eukaryotes, translation initiation factor 3 (elF3) is thought to play an essential role in this process by influencing mRNA and tRNA binding through indirect interactions on the backside of the 40S subunit. Here we show by directed hydroxyl radical probing that the human elF3 subunit elF3j binds to the aminoacyl (A) site and mRNA entry channel of the 40S subunit, placing elF3j directly in the ribosomal decoding center. elF3j also interacts with elF1A and reduces 40S subunit affinity for mRNA. A high affinity for mRNA is restored upon recruitment of initiator tRNA, even though elF3j remains in the mRNA-binding cleft in the presence of tRNA. These results suggest that elF3j functions in part by regulating access of the mRNA-binding cleft in response to initiation factor binding.