Uberbacher E C, Bunick G J
University of Tennessee-Oak Ridge Graduate School of Biomedical Sciences, Biology Division 37831-8077.
J Biomol Struct Dyn. 1989 Aug;7(1):1-18. doi: 10.1080/07391102.1989.10507747.
The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial direction. The 1.87 turn superhelix consists of B-DNA with about 78 base pairs or 7.6 helical repeats per superhelical turn. The mean DNA helical repeat contains 10.2 +/- 0.05 base pairs and spans 35 A, slightly more than standard B-DNA. The superhelix varies several Angstroms in radius and pitch, and has three distinct domains of curvature (with radii of curvature of 60, 45 and 51 A). These regions are separated by localized sharper bends +/- 10 and +/- 40 base pairs from the center of the particle, resulting in an overall radius of curvature about 43 A. Compression of superhelical DNA grooves on the inner surface and expansion on the outer surface can be seen throughout the DNA electron density. This density has been fit with a double helical ribbon model providing groove width estimates of 12 +/- 1 A inside vs. 19 +/- 1 A outside for the major groove, and 8 +/- 1 A inside vs. 13 +/- 1 A outside for the minor groove. The histone core is primarily contained within the bounds defined by the superhelical DNA, contacting the DNA where the phosphate backbone faces in toward the core. Possible extensions of density between the gyres have been located, but these are below the significance level of the electron density map. In cross-section, a tripartite organization of the histone octamer is apparent, with the tetramer occupying the central region and the dimers at the extremes. Several extensions of histone density are present which form contacts between nucleosomes in the crystal, perhaps representing flexible or "tail" histone regions. The radius of gyration of the histone portion of the electron density is calculated to be 30.4 A (in reasonable agreement with solution scattering values), and the histone core volume in the map is 93% of its theoretical volume.
已使用8埃分辨率的衍射数据确定了核小体核心颗粒的X射线晶体结构。该颗粒的平均直径为106埃,在超螺旋轴方向上的最大厚度为65埃。穿过组蛋白核心的最长弦长为85埃,且方向不与轴平行。1.87圈的超螺旋由约78个碱基对的B型DNA组成,即每超螺旋圈有7.6个螺旋重复。平均DNA螺旋重复包含10.2±0.05个碱基对,跨度为35埃,略大于标准B型DNA。超螺旋的半径和螺距变化数埃,并有三个不同的曲率区域(曲率半径分别为60、45和51埃)。这些区域与颗粒中心相隔局部更尖锐的弯曲,分别为±10和±40个碱基对,导致整体曲率半径约为43埃。在整个DNA电子密度图中,可以看到内表面超螺旋DNA沟的压缩和外表面的扩张。该密度已与双螺旋带模型拟合,得出大沟内宽度估计为12±1埃,外为19±1埃,小沟内为8±1埃,外为13±1埃。组蛋白核心主要包含在超螺旋DNA所界定的范围内,在磷酸主链朝向核心处与DNA接触。已定位了旋回之间密度的可能延伸,但这些低于电子密度图的显著性水平。在横截面上,组蛋白八聚体的三方组织很明显,四聚体占据中心区域,二聚体在两端。存在几个组蛋白密度的延伸,它们在晶体中形成核小体之间的接触,可能代表灵活的或“尾巴”状的组蛋白区域。电子密度图中组蛋白部分的回转半径经计算为30.4埃(与溶液散射值合理一致),图中组蛋白核心体积为其理论体积的93%。