The view is toward the interface between the 30S and 50S subunits. 23S rRNA is colored gray; 5S rRNA is colored white. The proteins are colored by Chain ("rainbow colors"). 23S RNA nucleotides at the peptidyl transferase center are colored red; the active site adenosine (A2451) is labelled "PTC".
(The published coordinates, 1giy.pdb, specify the atomic postitions for the tRNAs and the mRNA; otherwise, only the alpha carbons of proteins or phosphorous atoms of rRNA are known. Therefore, Backbone (thick and thin) or Spacefill are the only displays used.)
The numbered "Highlight" buttons above display details of the 30S structure. The following paragraphs briefly describe the displays.
1. RNA and Protein Features.
a. The 23S rRNA domains are thick backbone, colored as follows: blue, 5' domain; magenta, central domain;red, 3' major domain; and yellow, 3' minor domain. Proteins are red. In contrast to the 30S subunit, where the RNA domains corresponded to discrete structural units, the RNA domains here interdigitate to form a unified whole.
b. The tRNAs are thick backbone; the A, P, and E sites are colored green, magenta, and orange, respectively. mRNA (U6) is colored to match the tRNA anticodons.
c. The protein subunits are colored Group and labelled at their N-termini.
2. Interactions
a. The Intersubunit Bridges are primarily RNA-RNA interactions.
L2, L5, L14, and L19 are the only large subunit proteins that interact
with the 30S subunit. The individual residues are Spacefill; RNA is colored
white, and protein is colored yellow. See Yusupov, et al. Table 2 for details.
b. The tRNA-50S Subunit Contacts are also largely RNA-RNA;
L1, L5, and L16 are the only proteins involved. For the following three
buttons, the 50S residues making contacts are Spacefill; RNA is white;
protein is yellow. The tRNA residues making these contacts are Spacefill,
colored cyan. See Yusupov, et al. Table 3 for details.
The P-Site tRNA contacts several L5 residues. The
other contacts are to 23S rRNA.
The A-Site tRNA contacts two residues of L16. The
amino acid acceptor ends of the P-site and A-site tRNAs extend into the
PTC.
The E-Site tRNA contacts relatively large portions
of L1 and L33 (not shown).
Viewing Tip: After highlighting the protein residues above,
select the chain and color it yellow to see the extended shapes of many
of them. For example, the sequence of Chime menu steps might be: Select¬Chain¬P;
then Select¬Change Color To¬Yellow.
The 25 protein and RNA chains in the 50S model are coded with uppercase letters. The complete listing of chains and standard subunit names is on a separate (pop-up) page, 50S Ribosome Chain and Subunit Terminology.
Page Top
The 50S subunit structure is described in Yusupov, M.
M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J.
H. D., Noller, H. F. (2001) "Crystal structure of the ribosome at 5.5 Å
resolution" Science 292:883. PubMed.
