RNA和RNA组学（RNomics)研究进展-shutcm.ppt

RNA和RNA组学（RNomics)研究进展 Figure 2. Experimentally phased electron density maps of the substrate analog complexes at 3.2???resolution, with models superimposed (oxygen, red; phosphorus, yellow; nitrogen, blue; carbon, green for rRNA and gray for substrate). (A) An Fo(complex) -?Fo(parent) difference electron density map with a skeletal model of CCdA-p-Puro superimposed. The CCdA corresponds to the 3 CCA of tRNA bound to the P-site. (B) A stereo representation of the 2Fo(complex) -?Fo(parent) electron density map of the CCdA-p-Puro in the active site region with the structures of the ribosome and inhibitor superimposed showing the proximity of the N3 of A2486 (A2451) to the nonbridging oxygen of the inhibitor phosphoramide in this complex. (C) An Fo(complex) -?Fo(parent) difference electron density map of the tRNA acceptor stem analog with a skeletal model of CCPuro superimposed. There is density only for the ribose and phosphate of C74 of the RNA hairpin. The CCPuro corresponds to a tyrosyl-3 CCA of tRNA in the A-site. Figure 3. A combined model of the CCA portion of the mini-helix bound to the A-site and CCdA-p-Puro bound to the A- and P-sites color coded as in Fig. 2. (A) The base-pairing interactions between the P-site C74 and C75 and the P-loop (green) of 23S rRNA on the left and the A-site C75 with the A-loop (purple) of 23S rRNA on the right. The catalytic A2486 (A2451) is near the phosphate oxygen (P) that is the analog of the tetrahedral intermediate oxyanion. (B) A view showing A2637 (A2602) (in all red) lying between the two CCAs and A2486 (blue), whose N3 approaches a nonbridging phosphate oxygen. The N1 atoms of the A76 bases from the A- and P-site tRNAs make nearly identical interactions with a ribose 2 OH in both the A- and P-loops, respectively, and an approximate twofold axis relates these residues. The U2620 (U2585) (gray) hydrogen bonds to the 2 hydroxyl of the A-site A76 ribose. Figure 4. A space-filling model of the 23S and 5S rRNA, the protein