X-ray structure of the T. thermophilus ribosome in complex with tRNA and mRNA at 3.5 Å resolution. The E site binds tRNA^Phe and the A and P sites bind Phe–tRNA^Phe (in which the O atom forming an ester linkage from Phe to O3' of the 3' terminal A has been replaced by an NH group to prevent the hydrolysis of the Phe–tRNA linkage).
(a) The RNA components of the ribosomal complex (its proteins are omitted for clarity) drawn in paddle form except for the 11-residue mRNA, which is shown in space-filling form. The 16S RNA is cyan, the 23S RNA is yellow, the 5S RNA is blue, the tRNAs in the A, P, and E sites are green, purple and red, and the mRNA, which is largely occluded by the 16S RNA, is colored according to atom type with C pink, N blue, O red, and P orange.
(b) The 16S RNA in interface view with its bound tRNAs and mRNA, all represented as in Part a.
(c) The 23S RNA in interface view (rotated 180° about the vertical direction relative to Part b) with its bound tRNAs all represented as in Part a.
(d) The interactions of the tRNAs with the mRNA. This assembly is drawn and colored as in Part a but with the mRNA shown in paddle form in orange. The Phe residues appended to the A- and P-site tRNAs are represented in space-filling form. Note the close approach of these Phe residues and that the tRNAs in the A and P sites, but not that in the E site, form based paired codon–anticodon interactions with the mRNA. [Based on an X-ray structure by Venki Ramakrishnan, MRC Laboratory of Molecular Biology, Cambridge, U.K. PDBids 2WDK and 2WDL.]