Figure 3.

Comparison of the DNA structures between human and X.laevis NCPs. The best superposition between human (yellow) and X.laevis (light blue; PDB code 1KX3) (11) NCPs, based on the histone octamers alone, reveals the discrepancy in the DNA structures. (A and B) Partial NCP structure, viewed as the upper display in Figure 1, but showing only 77 bp and associated proteins. The black arrows indicate the directions and ranges of the consecutive 1 bp shifts to the 3′-side, in comparison with the DNA in Xla-NCP. The pink, orange and green circles correspond to those in Figures 2A and 4A. Each SHL label of −1 to −7 or 1 to 7 represents one further DNA double helix turn from SHL0, which is located at the central base pair numbering as zero in Figure 2A. The close-up inset indicates a H2B tail, whose positional change may induce the local alteration of the DNA path. In the close-up stereo view, all of the atoms of a human NCP are shown as normal sticks, where the phosphorus, oxygen and nitrogen atoms are colored cyan, red and blue, respectively, and all of the Xla-NCP atoms are shown as light blue sticks. (C) The side stereo view, corresponding to the lower display in Figure 1, but representing the superhelical DNA pathway alone. The broken ellipsoids, shadowed yellow and light blue, represent the space between two DNA duplexes within human and X.laevis NCPs, respectively. The black arrows indicate the expanding distance between the same sugar–phosphate backbones of two NCPs.