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QDE-1 ΔN Surface Architecture

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posted on 21.02.2013, 13:01 by Paula S Salgado, Minni R. L Koivunen, Eugene V Makeyev, Dennis H Bamford, David I Stuart, Jonathan M Grimes

(A) Surface charge representation of subunit A of QDE-1 ΔN (subunit B coloured grey). Blue arrow indicates proposed RNA product groove; red arrow indicates proposed NTP tunnel; and purple arrow indicates tunnel linking active sites in the dimer. The Mg2+ ions are shown as green spheres. Left panel: dimer (view similar to Figure 1A). Right panel: sliced view of left panel to reveal the tunnels.

(B) Different conformations of QDE-1 ΔN subunits modify polymerase active site accessibility. Left panel: cartoon representation of superposition of observed subunit conformations, coloured according to domain definition: subunit A as in Figure 1A; subunit B: slab, cyan; catalytic, magenta; neck, wheat; and head, yellow; C2 crystal form subunit (semi-transparent): slab, marine; catalytic, violet; neck, light salmon; and head, orange. In all panels, Mg2+ ions are represented as green spheres. The direction of the movement of the slab and head domains is indicated by grey arrows, and the non-crystallographic 2-fold is shown. Central and right panels: RNA-DNA duplex (from an elongation complex of yeast RNApolII) fitted (using the operators for superposition of yeast RNApolII onto QDE-1) into QDE-1 ΔN closed and open subunits (represented as molecular surfaces). Centre panel colours subunit A (closed conformation). Right panel shows a view rotated by 180° with subunit B (open conformation) coloured. RNA-DNA duplex model is show in ball-and-stick representation.

(C) Close-up of the duplex model from (B). Domains are coloured as for the central panel of (B). The slab domain of molecule A would lie across the front of the figure and has therefore been removed for clarity.

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