Figure 4.

Analysis of the density in the central cavity of the RSC–nucleosome reconstruction and comparison with the X-ray structure of the nucleosome. (a) A top view of the RSC–nucleosome complex (left) showing only a central slab (denoted by the broken rectangle in Figure 3b) that includes density resulting from nucleosome binding. Density presumably corresponding to the histone core (shown in solid blue) comes into close contact with RSC density (shown in yellow and gray) in several places. Non-RSC density adjacent to the central histone density is rendered as a semitransparent light blue surface. The distribution of density resulting from nucleosome binding is best appreciated after the removal (by difference mapping) of RSC density (right). (b) Comparison of presumed histone density with a low-resolution (25 Å) model of the histone core derived from its X-ray structure³⁹ shows a close correspondence in shape and size. In these views, the histones are shown in space-filling representation: H2A, yellow; H2B, red; H3, blue; H4, green. See text for details. (c) The same slabbed top view of the RSC–nucleosome structure shown in a but with a model of the histones docked in place. RSC densities in close contact with the nucleosome are designated 1–3. The proximity of density 1 to the dyad suggests that it probably corresponds to the Sth1 ATPase subunit. Absence of DNA density around the dyad suggests that binding of Sth1 pulls DNA away from the histones (as indicated by the red arrow), which would explain the origin of a reported DNase I hypersensitivity site near the dyad generated by RSC binding in the absence of ATP¹⁰. Possible changes in the arrangement of nucleosomal DNA are schematically represented by a black line, with regions where no DNA density is apparent in the RSC–nucleosome reconstruction shown with a broken line.