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Figure 2.
Figure 2. Updating the Pol II Model According to the Zn-MAD
Densities
(A–C) (A) Definition of the loop structure at
the tip of a two-helix stalk in Rpb2. Poly-alanines (green, Cα
only) were fitted into the density, connecting the helices.
Electron densities (red) are shown all at 1.0σ level for
(A)–(C). The existing model of Pol II (Cα only) is colored
blue in (A)–(C). Some of the side chain densities that
projected off the α carbons were evident in the 4.1 Å
Zn-MAD map. (B) The model for Rpb4 was updated according to the
Zn-MAD densities. Residues 118–126 were adjusted to fit the
density. Residues 113–117 were inserted according to the
density. α carbons of the updated residues are shown in green.
Again, partial densities of certain side groups protrude from
the α carbons. (C) Localization of fork loop-1 (green, Cα
model) according to its Zn-MAD density. Clear densities occurred
at a site opposite the rudder over the cleft, and they could
only be accounted for by fitting with fork loop-1. As shown by
the touching densities, fork loop-1 contacts the rudder to form
a set of “arms” that surrounds the DNA/RNA hybrid in the
ternary complex as has been noted (Westover et al., 2004b).
Residues involved in the contact are indicated. The bridge helix
defining the floor of the cleft is indicated as well.
(D
and E) (D) A motion by fork loop-1 can be seen from its
different locations in the free Pol II (red, Cα model) and in
ternary complexes (yellow and purple). The view is roughly from
the downstream side through the cleft and against the wall (not
visible here) of the hybrid tunnel. The rudder is shown in cyan,
and the rest of Pol II is shown in blue. The DNA template strand
is shown by the gray stick model, while the transcript RNA is
indicated by the pink sticks. The downstream DNA (gray sticks)
is roughly perpendicular to the plane of the paper. The dashed
line indicates a cut-away plane against which is the viewing
direction for (E). (E) Compartmentalization of the Pol II cleft
by the protein mass of fork loop-1 (red) and the rudder (white).
This is a cut-away view from the plane, as indicated in (D),
against the clamp domain of Rpb1. The surface rendering shows
the spatial arrangement of the hybrid tunnel and the downstream
DNA channel.
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