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Figure 1.
Figure 1. The UvrB–DNA complex and selected electron density.
(a) Surface of UvrB is color-coded by domain (yellow, 1a;
green, 1b; blue, 2; red, 3; cyan, the  -hairpin
of UvrB; magenta, the newly formed -sheet
after DNA binding). DNA is illustrated by spokes and letters,
color-coded by nucleotide type. The letter representation of the
DNA is in a similar orientation to the DNA in the structure.
Black letters, disordered nucleotides; F, fluorescein-adducted
thymine. The fluorescein-dT, although partially ordered (Fig.
1b), has been omitted from the figure for clarity. (b) 2F[o] -
F[c] electron density map contoured at 1.0  covering
the DNA. Gray, carbons of unmodified nucleotides; green, carbons
of partially ordered fluorescein; magenta, electron density for
the fluorescein. Nucleotides are labeled consecutively from 5'
to 3', omitting numbers of disordered residues. (c) UvrB–DNA
model showing how the inner strand of the DNA (red) travels
between the -hairpin
(cyan) and domain 1b and the outer strand (green) travels around
the outside of the -hairpin.
(d) Superposition of DNA-bound and apo UvrB. -hairpin
regions of the DNA-bound (cyan and blue) and apo UvrB (PDB entry
1D9X; yellow and gold) are superimposed. Select residues are
shown with color-coded labeling. Dark gray spokes represent the
bound DNA and the surface of the remainder of the UvrB–DNA
complex is shown in gray.
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