Fig. 6: Structure of ZIM-1 ZF1-2-CTD in complex with chromosome II/III PC DNA.

a ITC experiments reveal the preferential binding of ZIM-1 ZF1-2-CTD (depicted in red) to the 11-bp chromosome II/III PC motif over motifs from other chromosomes (X chr, chr V, and chr I/IV). b Depiction of the overall structure of ZIM-1 ZF1-2-CTD in complex with the 11-bp chromosome II/III PC motif. ZF1, ZF2, and CTD are colored in pale green, wheat, and dirty violet, respectively. The top strand and bottom strand are represented in deep salmon and gray, respectively. c Structural superposition of ZIM-1 ZF1-2-CTD and HIM-8 ZF1-2-CTD alignment using their ZF1 domains within the overall structure reveals an RMSD of 2.4 Å, suggesting an altered ZF2 docking geometry. d General schematic diagram illustrating the detailed base-specific interactions between ZIM-1 ZF1-2-CTD and the 11-bp chromosome II/III PC DNA sequence. Color codes for ZF1, ZF2, and elements of the top and bottom strands adhere to those defined in (b). Direct hydrogen bonds are represented in blue, while Van der Waals contacts are depicted with orange dashed lines. e–g Further highlighting base-specific contacts of ZF1 at the atomic level, with interatomic distances measured in angstroms. h The side chain of ZIM-1 ZF1 R480 (−4) recognizes the G at the base pair 4 on the chromosome II/III PC motif TTGG sub-site. However, the side chain of HIM-8 ZF1 R262 (−4) corresponding to ZIM-1 ZF1 R480 (−4) recognizes the A at base pair 7 and the G at base pair 8, but not the G at the base pair 4 on the X chromosome motif. i, j Further highlighting base-specific contacts of ZF2 at the atomic level, with interatomic distances measured in angstroms.