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Figure 2.
Figure 2. Model and EM Features of the Pol I Core
(A)
Placement of the Pol II ten-subunit core structure (Armache et
al., 2005) (gray) into the EM density (blue). The foot was
deleted, and subunits Rpb5, Rpb8, and Rpb9 are highlighted in
magenta, green, and orange, respectively. The clamp has been
fitted as a separate rigid body.
(B) Fit of the common
subunits Rpb5 and Rpb8 to the EM map, and density for the core
subunit A12.2 (the Pol II homolog Rpb9 is shown as a ribbon
model).
(C) Pol II structure-guided sequence alignment of
the five Pol I subunits with homologs in Pol II (compare Table
1). The domain organization of Pol II subunits Rpb1, Rpb2, Rpb3,
Rpb11, and Rpb9 is shown as diagrams (Cramer et al., 2001).
Insertions and deletions exceeding five amino acid residues are
indicated. Conserved folds are indicated by orange highlighting
of the bar above the diagrams. For details see Figure S1.
(D) View of the core Pol II structure (Cramer et al., 2001) from
the side, with domains depicted in (E) highlighted.
(E) Pol
I-specific structural elements. Fitted Pol II elements are shown
as ribbon models. Insertions and deletions explaining the EM
density are named according to (C). The clamp head is in light
red and the clamp core in red. The dock and foot domains are in
beige and blue, respectively, and Rpb3, Rpb10, and Rpb11 are in
red, dark blue, and in yellow, respectively. Zinc ions are
depicted as marine spheres.
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