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Figure 2.
FIGURE 2. Calculation of a quasi-atomic model for
EV12·DAF. A, variation in SCR2 orientation for the 14
crystal forms of DAF[1234], with each model superimposed onto
the capsid-docked SCR3. Only SCR2 is shown for each model. B,
variation in SCR2 orientation for the 43 different NMR models.
C, the optimal SCR2 position is from chain B of the x-ray
structure of Protein Data Bank code 1OK3 [PDB]
. D, points of contact on DAF[1234] with the symmetry partner
across the 2-fold axis. The green surface represents a steric
clash between Arg^102 and Arg^103 and identical residues of the
symmetry partner. This is resolved by side chain rearrangement.
The blue surface is a van der Waals contact between Pro^137 and
Pro^109 of the symmetry partner. The red and orange surfaces are
an overlap between the main chain atoms of residues 174-180 of
SCR3 (red) and a surface composed of residues 95-98 and 75-77 of
the symmetry partner SCR2 (orange). This clash can be resolved
only by a remodeling of loop 174-180. E, electron density of
SCR1. The strong density at the center of each lobe is shown as
a red mesh, whereas the lower contours are shown as a blue mesh.
The major and minor lobes, as well as the position of SCR2, are
highlighted. F, superposition of all 14 possible SCR1
orientations from the crystal structures. These orientations are
consistent only with the minor lobe density. G, optimal "minor
lobe" SCR1 model from the side. Also highlighted is the
remodeled loop 174-180 on SCR3. H, complete DAF model based on a
hybrid of the original DAF[34] fit (with the remodeled loop
174-180 on SCR3) and the two crystal structures that gave
optimal SCR1 and SCR2 positions (green). Also shown in magenta
is the alternative position for SCR1 proposed to explain the
major lobe density. The symmetry partner DAF molecule is shown
in red. I, radially depth-cued atomic model of the virus capsid
(blue) decorated with 60 copies of the DAF[1234] hybrid model
(green).
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