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Figure 3.
Figure 3. Comparison of the three-dimensional conformations
of Ub[2] in solution derived here at (a) acidic pH and ((b) and
(c)) at neutral conditions. For comparison, (d) shows the
crystal structure of Ub[2].[13.] Structures shown in (a) and (b)
were derived using 15N relaxation data (rotational diffusion
tensor) while that in (c) is on the basis of RDCs (alignment
tensor). The orientation of the principal axes of the rotational
diffusion or alignment tensors of the Ub[2] molecule, seen by
each individual Ub domain, is indicated by rods positioned at
the center of mass of the corresponding domain. The z-axes
(turquoise) are oriented in the horizontal direction, the y-axes
(pink) are vertical, and the x-axes are oriented toward the
reader. Structures for the individual domains are from
1aar.pdb;[13.] a similar orientation was obtained using other
protein coordinates (see the text). The domains are colored
green (proximal) and blue (distal). Cylindrical arrows (red)
indicate the orientation of a-helices. The location of L8, I44,
and V70 in both domains, as well as that of K48 in the proximal
domain are indicated in (b). Because this approach provides the
orientation (not the distance) between the domains, their
relative positions in (a)-(c) are somewhat arbitrary. Also, the
C terminus of the distal domain is unstructured/flexible and
should easily adopt a conformation accommodating closer contact
between the units. Its conformation shown here is from the
crystal structure and should be considered as an illustration
only. The picture was prepared using Molmol. [44.]
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