The 23S and 5S rRNA are shown in the "rotated crown view" orientation, i.e. from the perspective of the 30S subunit. The display is Backbone with the "standard domain colors" used in the Ban, et al. paper. The active site residues in the peptidyl transferase center ("PTC") are colored gold. The initial display has phosphorus atoms, only.
The "Load..." buttons show each of the domains initially in the rotated crown view orientation as a thick backbone using the standard domain colors. After a short delay, the bases are displayed as Sticks, colored CPK; the backbone is shown in wireframe with a thick Trace, colored Group, i.e."rainbow colors" with the 5' end, blue and the 3' end, red. These are all-atom models that can be displayed and colored with all of the Chime menu selections.
For example, to view the full backbone structure, use this sequence of Chime menu steps: Select¬Nucleic¬Backbone; then Display¬Sticks (or any of the other seven choices).
- Some Domain Features
- Domain I: Residues 10-531; helices 1-24. Located on the back of the subunit.
- Domain II: Residues 532-1366; helices 25-46. Largest of the seven domains.
- Domain III: Residues 1367-1723; helices 47-60.
- Domain IV: Residues 1724-2063; helices 61-71. Contains most of the 30S subunit contacts.
- Domain V: Residues 2063-2663; helices 72-94. Peptidyl transferase center; EF-G binding site.
- Domain VI: Residues 2667-2914; helices 95-101. Saracin-ricin loop in helix 95.
- 5S RNA: Residues 4-120; helices 1-5.
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The 50S subunit structure is described in Ban, N., Nissen, P., Hansen, J., Moore, P. B., Steitz, T. A. (2000) "The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution." Science 289:905. PubMed [1ffk.pdb].
The model shown here used coordinates from Klein, D. J., Schmeing, T. M., Moore, P. B., Steitz, T. A. (2001) "The Kink-Turn: A New RNA Secondary Structure Motif." Embo J. 20:4214 PubMed [1jj2.pdb].
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