Figure 1.

Color-coded representation of the DNA sequences crystallized in known nucleosome core-particle structures (2-20). The Protein Data Bank identifiers (PDB_IDs) of individual structures are noted on the left in the same order as in Table 1, with the entry for the currently best-resolved structure (1kx5) highlighted by triangles. Nucleotide positions are reported with respect to the central base pairs of the crystallized 147-bp sequences at position 0. The small numerals above the mosaic denote the base-pair position, and the large numerals above the canonical B-DNA structure show the superhelical position, i.e., the approximate number of helical turns of a given base pair from the dyad (2). The double-helical image shows the relative orientation of the base pairs and the directions of the major/minor grooves at each sequential position — e.g., the long axis of the base-pair points toward the viewer, the major groove faces downward, and the minor groove faces upward at the dyad and all other integral superhelical positions. Nucleotide content in individual structures is depicted on the right with the same color-coding as that along individual sequences. The ‘missing’ bases in nucleosomes that bind 145- and 146-bp DNA fragments are represented in black and positioned to maximize the alignment of the sequences with the bases in the 147-bp chains. Overrepresented dinucleotide steps include AA·TT, AT·AT, and CA·TG. Underrepresented dimers include CG·CG, AC·GT, TA·TA, and GG·CC. Image does not include the bases in the most recently solved core-particle structure (21), with DNA identical in sequence to that in the one other nucleosome binding a 145-bp piece of DNA (17). See Table 1 for details of nucleosome composition and resolution.