Comparison of X-ray structures of the nucleosome core particle in two different hydration states

The X-ray structure of the nucleosome core particle was determined at 7 A resolution using crystals containing mixed-sequence DNA and 21% to 27% of 1,6-hexanediol (partially dehydrated crystals). The alcohol was added to the crystals after growth to overcome the non-isomorphism of the crystals and improve the quality of their X-ray diffraction. Here, we report the structure of the nucleosome core particle from these crystals in the absence of the alcohol 1,6-hexanediol at 9 A resolution. The structure, under conditions of nearly full hydration, has been solved by multiple isomorphous replacement methods employing multiple heavy-atom compounds identical to those used for the partially dehydrated structure. The electron density of particles in the two crystal structures is well-correlated throughout the maps and structural elements of the DNA superhelix and histone proteins are generally similar, e.g. the DNA bends sharply at positions +/- 1 and +/- 4 double-helical turns from the DNA center. These results rule out the occurrence of gross structural changes in the 7 A structure due to addition of alcohol. The parts of the nucleosome core particle structure, which are dissimilar between the two forms, can be attributed to differences in molecular packing induced by the addition of 1,6-hexanediol. In contrast to the structure seen in the partially dehydrated crystals, the fully hydrated crystals show a particle in which the H2A-H2B dimers are symmetrically related by the dyad axis found in the H3-H4 tetramer region. However, in the fully hydrated crystals, the first and last double-helical turns of DNA superhelix are not related by dyad symmetry, and one of these segments has reduced contact with the adjacent H2A-H2B dimer.