Another MDFF application has been recently published by the Roland Beckmann group (University of Munich, Germany). Their publication describes two cryo-EM structures of eukaryotic ribosomes stalled by regulatory peptides.
Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide. Shashi Bhushan, Helge Meyer, Agata L. Starosta, Thomas Becker, Thorsten Mielke, Otto Berninghausen, Michael Sattler, Daniel N. Wilson, and Roland Beckmann. Mol. Cell, 40, 138-146, 2010.
Specific regulatory nascent chains establish direct interactions with the ribosomal tunnel, leading to translational stalling. Despite a wealth of biochemical data, structural insight into the mechanism of translational stalling in eukaryotes is still lacking. Here we use cryo-electron microscopy to visualize eukaryotic ribosomes stalled during the translation of two diverse regulatory peptides: the fungal arginine attenuator peptide (AAP) and the human cytomegalovirus (hCMV) gp48 upstream open reading frame 2 (uORF2). The C terminus of the AAP appears to be compacted adjacent to the peptidyl transferase center (PTC). Both nascent chains interact with ribosomal proteins L4 and L17 at tunnel constriction in a distinct fashion. Significant changes at the PTC were observed: the eukaryotic-specific loop of ribosomal protein L10e establishes direct contact with the CCA end of the peptidyl-tRNA (P-tRNA), which may be critical for silencing of the PTC during translational stalling. Our findings provide direct structural insight into two distinct eukaryotic stalling processes.