The 23S rRNA (orange), 5S rRNA (magenta) and protein (blue) are shown as thick Backbone. A few proteins are labeled for orientation. The active site residues in the peptidyl transferase center ("PTC") are colored gold. The displays have RNA phosphorus atoms and protein alpha carbons, only.
The exit tunnel extends from the PTC and opens at the back of the subunit. The tunnel walls are primarily RNA loop residues from domains I-V. In addition, non-globular portions of proteins L4 (Chain C), L22 (Chain O), and L39a (Chain Y) also line the tunnel. The diameter varies from 15-20 Å; the average is 15 Å.
The exiting polypeptide is modelled as a polyalanine helix of 61 residues (Chain 3).
The "Highlight" buttons show progressively closer views of the tunnel and nascent polypeptide chain.
1. 23S RNA Domains (I-VI) are shown with "standard domain colors" used in Fig. 4 of the Ban, et al. paper. The proteins are thin Backbone.
2. Exit Tunnel Residues, colored cyan, are those listed by Nissen et al. in Fig. 11. The exiting peptide is thick Backbone, colored red.
3. Closest Contacts (within 12 Å of the exiting peptide) are colored yellow; the other exit tunnel residues are green.
4. Zoom The four PTC nucleotides are gold, Spacefill.
Rotate -90 and choose Slab Mode for a side view of the exit tunnel.
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The 50S subunit structure is described in two papers:
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].
Nissen, P., Hansen, J., Ban, N., Moore, P. B., Steitz, T. A. (2000) "The structural basis of ribosome activity in peptide bond synthesis." Science 289:920. PubMed [1ffz.pdb & 1fg0.pdb].
The coordinates of the exiting polyalanine were generously provided by Dr. Poul Nissen. The displays correspond roughly to Fig. 11 of the Nissen et al. paper.
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