The many interactions of tRNA with the ribosome
are fundamental to protein synthesis. During the peptidyl
transferase reaction, the acceptor ends of the aminoacyl
and peptidyl tRNAs must be in close proximity to allow
peptide bond formation, and their respective anticodons
must base pair simultaneously with adjacent trinucleotide
codons on the mRNA. The two tRNAs in this state can be
arranged in two nonequivalent general configurations called
the R and S orientations, many versions of which have been
proposed for the geometry of tRNAs in the ribosome. Here,
we report the combined use of computational analysis and
tethered hydroxyl-radical probing to constrain their arrangement.
We used Fe(II) tethered to the 5′ end of anticodon
stem-loop analogs (ASLs) of tRNA and to the 5′ end
of deacylated tRNAPhe to generate hydroxyl radicals
that probe proximal positions in the backbone of adjacent
tRNAs in the 70S ribosome. We inferred probe-target distances
from the resulting RNA strand cleavage intensities and
used these to calculate the mutual arrangement of A-site
and P-site tRNAs in the ribosome, using three different
structure estimation algorithms. The two tRNAs are constrained
to the S configuration with an angle of about 45° between
the respective planes of the molecules. The terminal phosphates
of 3′CCA are separated by 23 Å when using the
tRNA crystal conformations, and the anticodon arms of the
two tRNAs are sufficiently close to interact with adjacent
codons in mRNA.