2.7 | Other ensemble targets
The RNA/protein complex (T1189/R1189 and T1190/R1190) determined by cryo-EM is the first target of this type in CASP. Image reconstructions from two sets of selected particles from the same sample yielded two different complexes, one with a single RNA molecule and six copies of the protein (TR1189) and the other a single RNA with four copies of the protein bound (TR1190). The experimental RNA conformations of the two targets are similar but may be influenced by the presence of the proteins, so requiring modeling of the protein and RNA together. There are no models with accurate RNA conformations or the correct positions of the bound proteins. It is likely that at the time of CASP15, no group had methods sufficiently mature to tackle hybrid complexes of this sort. Recent developments suggest that by the next CASP such methods may be available for testing (24).
The final ensemble example is for a series of time resolved structures of a Holliday junction branch migration machine (25), T1170, H1171 (v1, v2), H1172 (v1-4). This is a large (~650 kDa) and complex target. The core is six sequence-identical subunits that form an asymmetric hexamer. As the machine goes through an ATP and protein binding-driven cycle, two of the subunits undergo significant interdomain movements deviating by as much as 3Å in different states, providing a basis for ensemble evaluation, while the rest of the structure is largely unchanged. However, the vast majority of submissions had symmetrical hexamers, so could not be evaluated for the conformational change. For those submissions with asymmetry, none had accurate structures of the conformationally variable subunits in any of the states.