Nucleic Acids Res
January 1, 2005;
Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle.
Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 A crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location -5.0 to -2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA-DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail
induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.
Nucleic Acids Res
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Figure 1. The overall structure of a human NCP. The upper ribbon model is the crystal structure of a human NCP. The arrow above NCP indicates a pseudo 2-fold axis passing through the center of the structure. The bottom figure displays the axial view of the particle. Histone chains are colored blue for H3, green for H4, yellow for H2A and red for H2B. The DNA is shown in ribbon traces for the 146 bp DNA phosphodiester backbones (brown for the I chain and forest green for the J chain). The Mn2+ and Cl− ions are depicted by cyan and silver balls, respectively.
Figure 2. Comparison of the DNA parameters between human and X.laevis NCPs. (A) B-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 X.laevis NCPs. The base pair numbers (−72 to 73) and SHL (−7 to 7) labels are the same as those in the earlier structures (11,12). 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). B-factors (Å2) are plotted for the 5′ phosphate group of each base (brown for the I chain and forest green for the J chain). Mn2+ 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 X.laevis NCPs (PDB code 1KX3) (11), 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 X.laevis (light blue line) nucleosomal DNA, respectively. The pink, orange and green ellipsoids of the twist parameters represent the corresponding regions illustrated by those in Figures 3A and B and Figure 4A. (B–D) 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 X.laevis (light blue; PDB code 1KX3) (11) NCPs, based on the histone octamers alone. Numbers presented for each base pair are the same as those in Figure 2A.
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.
Figure 4. Crystal packing of human NCP. (A) The upper stereo model shows the human NCP crystal packing, viewed approximately perpendicular to the crystallographic c-axis. The bottom figure displays the side view of the same molecular arrangements. Short arrows show the approximate locations of the three crystallographic axes. Only the DNA backbone is shown for clarity. The pink, orange and green circles are equivalent with the regions illustrated by those in Figures 2A and Figures 3A and B. The black arrows indicate the directions and ranges of the consecutive 1 bp shifts to the 3′-side. (B–D) The close-up stereo views of the boxed area in (A) show the discrepancy in the DNA structures by the superposition between human (yellow) and X.laevis (light blue; PDB code 1KX3) (11) NCPs, based on the histone octamers alone. The gray arrows represent the modification of the DNA pathway by the inter-particle collides.
Figure 5. Details of the DNA–DNA contact within the human NCP crystal. (A) Detailed stereo view of the DNA–DNA contact shown in Figure 4B and C. (B) Detailed stereo view of the DNA–cation–DNA contact shown in Figure 4D. All of the atoms of the DNA duplexes are shown as normal sticks, where the phosphorus, oxygen and nitrogen atoms are colored cyan, red and blue, respectively. The Mn2+ ions and the water molecules are depicted by black and red balls, respectively. Broken lines and distances between two atoms show possible interactions through water molecules. Numbers presented for each base pair are the same as those in Figure 2A.
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