3D modeling of ribosomal RNA using cryo-electron microscopy density maps

Ribosomes are macromolecular protein-RNA complexes translating mRNA
into protein. To date, crystal structures are available for the
bacterial 30S and archaeal 50S subunits, as well as the complete
bacterial 70S ribosomes. Eukaryotic ribosomes are much more complex
in terms of ribosomal RNA and proteins. However, to date
high-resolution crystal structures of eukaryotic ribosomes or
ribosomal subunits are lacking. In order to build reliable models
for the eukaryotic rRNA, we developed an approach for large scale
homology and de novo modeling of RNA and subsequent exible tting
into high-resolution cryo-EM density maps. Using this approach we
built a model of the T. aestivum and the S. cerevisiae ribosome
based on available cryo-EM maps at 5.5 Å and 6.1 Å resolution,
respectively. The model comprises of 98% of the eukaryotic rRNA
including all 21 RNA expansion segments (ES) and structurally six
variable regions. Further, we were able to localize 74/80 (92.5%)
of the ribosomal proteins. The model reveals unique ES-ES and
r-protein-ES interactions, providing new insight into the structure
and evolution of the eukaryotic ribosome. Moreover, the model was
used for analyzing functional ribosomal complexes, i.e. the
characterization of dierent nascent polypeptide chains within the
ribosomal tunnel, intermediates of protein translocation as well as
mRNA quality control.