The T. thermophilus 70S ribosome is shown as a Backbone display of its RNA and protein components. The initial ("standard") view is from the back of the 30S (small) subunit toward the 50S (large) subunit. Successive -90° rotations correspond to the views in Yusupov et al. Fig. 2 A-D.
The coloring is: cyan, 16S RNA; blue, 30S subunit proteins; gray, 23S RNA; blue, 5S RNA; magenta, 50S subunit proteins; gold, A-Site tRNA; orange, P-Site tRNA; red, E-Site tRNA; and green, mRNA (the U6 oligonucleotide).
The numbered "Highlight" buttons above display aspects of the ribosome architecture. The following paragraphs briefly describe the displays.
1. Ribosome Subunits.
a. The 50S (large) subunit is in the "standard view" with the 30S subunit removed. The active site residues are colored red and labeled "PTC" (peptidyl transferase center).
View the 23S and 5S RNAs alone; the 5' and 3' ends of 23S RNA are labeled. Proteins L1, L9, and L7/L12 are labeled at their N-termini in the Proteins, only view.
b. The 30S (small) subunit is rotated 180° from the "standard view" with the 50S subunit removed. View the 16S RNA alone; the 5' and 3' ends of 16S RNA are labeled. Proteins S6, S11, and S20 are labeled at their N-termini in the Proteins, only view.
In both views described above, the tRNAs and mRNA can be added to the display.
c. 70S Ribosome restores the original display.
2. Translation Steps
a. The Scripted Animation moves the tRNAs through three
cycles of peptide bond formation. Each functional step is labelled in the
display as the tRNA traverses the A, P, and E sites. After the initiator,
fMet, is added, successive amino acids are designated as "aa2", "aa3",
"aa4". Uncharged tRNAs are indicated with an "*" at their 3' ends. The
interval between steps is about 1 sec.
b. The One Cycle Stepwise buttons show the same functional
steps though one cycle of peptide bond formation, i.e. fMet-aa2 is formed
and the cycle ends with the dissociation of uncharged tRNAfMet.
Viewing Tip: View the translation steps (first) after restricting
the view to either the 30S or 50S subunits. Since the anticodon interacts
only with the 30S subunit and the charged CCA end interacts only with the
50S subunit, both views are informative.
Notes: 1. The coordinates used in this display have only the alpha carbons
of proteins (CA) and the phosphorus atoms of RNAs (P). Thus, Backbone and
Spacefill are the only Chime display options available. The original PDB
coordinates (1gix.pdb and 1giy.pdb) have atomic coordinates for the tRNAs
and the mRNA.
2. The 25 protein and RNA chains in the 30S model are coded with uppercase
letters. The 50S model uses lowercase letters. The complete listing of
chains and standard subunit names is on a separate (pop-up) page, 70S
Ribosome Chain and Subunit Terminology.
3. In both of the translation simulations, a "fictitious mRNA" was
added to the coordinate file that extends several nucleotides 3' and 5'
from the real mRNA analog in the published structure.
Page Top
The ribosome 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.
