Comparison of the DNA parameters between human and NCPs

• Main Authors: Tsunaka, Yasuo, Kajimura, Naoko, Shin-Ichi Tate, Morikawa, Kosuke
• Format: Still Image
• Language: unknown
• Published: figshare 2011
• Subjects: Molecular Biology; The Pointers
• Online Access: https://dx.doi.org/10.6084/m9.figshare.4834; https://figshare.com/articles/figure/Comparison_of_the_DNA_parameters_between_human_and_NCPs/4834

Copyright information: Taken from "Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle"Nucleic Acids Research 2005;33(10):3424-3434.Published online 10 Jun 2005PMCID:PMC1150222.© The Author 2005. Published by Oxford University Press. All rights reserved () -factors of phosphates, metal binding sites, r.m.s.d. values and twist base-pair-step parameter of the 146 bp DNA compared between human and NCPs. The base pair numbers (−72 to 73) and SHL (−7 to 7) labels are the same as those in the earlier structures (,). The primary bound-phosphate groups are indicated above the base sequence by the pointers showing the strand direction (dark, 3′→5′; light, 5′→3′) and the interacting histone motif (L1, loop1; L2, loop 2; A1, α1). -factors (Å) are plotted for the 5′ phosphate group of each base (brown for the I chain and forest green for the J chain). Mn binding sites are indicated above the base sequence by the yellow and light blue arrows (solid, binding the DNA major groove; broken, binding the DNA minor groove) in the structures of human and NCPs (PDB code 1KX3) (), respectively. The r.m.s.d. values below the base sequence were calculated by the superposition of 18 or 19 bp between two NCPs. The twist base-pair-step parameters were plotted as open circles and closed squares for the human (yellow line) and (light blue line) nucleosomal DNA, respectively. The pink, orange and green ellipsoids of the twist parameters represent the corresponding regions illustrated by those in and . (–) The simplified stereo model of the DNA duplexes in the regions surrounded by the ellipsoids in (A). The differences in helical twist are shown by the superposition between human (yellow) and (light blue; PDB code 1KX3) () NCPs, based on the histone octamers alone. Numbers presented for each base pair are the same as those in .