Fig. 6

Distribution of Ty1 cofactor ribosomal proteins on the structure of the S. cerevisiae ribosome. The structure of the yeast ribosome [69] is derived from structure files 3J78 deposited in the Protein Data Bank (PDB; http://www.rcsb.org/pdb/) [70]. The structure was modeled using the VMD Molecular Graphics Viewer (http://www.ks.uiuc.edu/Research/vmd/) [71]. The structure of the rRNAs are shown as a surface with the large subunit rRNAs colored blue and the small subunit rRNA colored cyan. The ribosomal proteins are shown in cartoon mode with those encoded by Ty1 cofactor genes in red (large subunit) or pink (small subunit) and all others in cyan (large subunit) or blue (small subunit). a The 80S subunit seen from A site side. b The 80S subunit rotated 180° to view from the E site side. c The 60S subunit showing the surface that is in contact with the 40S in the 80S complex. d The 40S subunit showing the 60S interface surface. e The end of the nascent peptide channel from the peptide exits showing Rps39 (in white) located immediately inside the end on the right side of the exit channel; beyond Rps39, deep within the exit channel, the tip of a loop on Rps4 can be seen (in red)