Figure 4. Target T1170, a Holliday junction hexamer (PDB: 7PBR).(A) superposition of two deformed chains versus (B)four undeformed chains in the same frame of reference. The domain that moves the most with respect to other two is encircled. (C)Grishin plots for the original target split into three domains show the similarity of results on domains 1, 2 and their combination 12 (left panel, points close to the diagonal), and the dissimilarity of results on the combined substructures 13 and 23 and their constituent domains (middle and right).
In all other targets, except for T1120, T1121 and T1170 discussed above, chains were largely similar, and the decision on domain splitting was dictated purely by Grishin plots. Below we discuss three cases of some of the most difficult domain rearrangements.
Target T1158 is a type IV ABC transporter, which is a common fold (see review 26). In CASP15, this protein family was represented by five targets - T1158 (Figure 5A) and T1158v1-v4, which differ by rigid body movements of the two halves of the transporter with respect to one another, and no significant rearrangements within the subunits (Figure 5B). When submitted to domain parsing programs, T1158 was split in several ways, none of which made functional sense. The suggested split was either too fragmented (6 domains by DDomain, or 5/8/7 by the top three SWORD assignments) or too coarse-grained (2 domains by DomainParser: the C-terminal globular domain (red) in Figure 5A (48-1022) and the rest). We split this target into two EUs (Figure 5C) reflecting the conformational changes that the transporter undergoes performing its biological function of opening and closing gates in bound and unbound states. In other words, evaluation units for T1158 were defined not from a single structure, but from a set of structures from the same superfamily. A Grishin plot for the target (not shown) supports the suggested split.