Human ribosomal proteins S5e and S16e are the homologues of prokaryotic S7p and S9p, respectively. It was shown that S5e and S16e are capable of the specific binding with a rRNA transcript corresponding to the region of human 18S rRNA containing helices H28-30 and H41-43 (3Dm), which is homologous to the region in 16S rRNA containing the entire binding site for S7p and the major part of the site for S9p. We have studied binding of S5e and S16e to 3Dm and demonstrated that while each of them is able to bind to the rRNA transcript independently, their simultaneous binding has a noticeable synergetic effect. Using enzymatic footprinting, we showed that these proteins protect 3Dm against hydrolysis with RNases mainly in the regions homologous to the sites of S7p and S9p binding on the 16S rRNA. At the same time, we found regions that correspond to 16S rRNA fragments distant from the binding sites of the respective homologous prokaryotic proteins. Comparison of these results with the data on 3Dm footprinting in binary complexes with S5e or S16e revealed that each of these proteins affects binding of another one to 3Dm, which is displayed in significant expansion of 3Dm sites protected by the proteins against hydrolysis in the ternary complex.