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Figure 6.
Fig. 6. Topology of the polymerizing complex, and location of
Rpb4 and Rpb7. (A) Nucleic acid configuration in polymerizing
(top) and backtracking (bottom) complexes. (B) Structural
features of functional significance and their location with
respect to the nucleic acids. A surface representation of pol II
is shown as viewed from the top in Fig. 3. To the surface
representation has been added the DNA-RNA hybrid, modeled as
nine base pairs of canonical A-DNA (DNA template strand, blue;
RNA, red), positioned such that the growing (3') end of the RNA
is adjacent to the active site metal and clashes with the
protein are avoided. The exact orientation of the hybrid remains
to be determined. The nontemplate strand of the DNA within the
transcription bubble, single-stranded RNA and the upstream DNA
duplex are not shown. (C) Cutaway view with schematic of DNA
(blue) and with the helical axis of the DNA-RNA hybrid indicated
(dashed white line). An opening in the floor of the cleft that
binds nucleic acid exposes the DNA-RNA hybrid (pore 1) to the
inverted funnel-shaped cavity below. The plane of section is
indicated by a line in (B), and the direction of view
perpendicular to this plane (side) is as in Fig. 3. (D) Surface
representation as in (B), with direction of view as in (C). The
molecular envelope of pol II determined by electron microscopy
of 2D crystals at 16 Å resolution is indicated (yellow
line), as is the location of subunits Rpb4 and Rpb7 (arrow,
Rpb4/7), determined by difference 2D crystallography (25).
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