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.