So, we went back to the cryo-EM data and analyzed the solvent shell density, independent of the model. There was excellent agreement between the two maps in the solvent shell indicating the cryo-EM data contained information about dynamic and complex water networks.

With Greg Pintilie, we updated SWIM, an algorithm which uses Segger to identify and model water and ions, to automatically model water and magnesium ions.

To stabilize these RNA complexes, each RNA forms many, interesting quaternary “bridges.” We found many of these bridges are conserved or covary in the RNA family.

Two of the most complex known RNA families, ROOL and GOLLD, are larger and more complex than thought, forming RNA nanocages. What might these microcompartments do in the cell?

The 6 helices of OLE form a bundle of pipes, whose loops weld together at a dimer interface. Known protein-binding motifs surround the outside of this bundle suggesting this RNA-protein complex may be RNA-scaffolded!