|
Figure 5.
Fig. 5. Arrangement of the downstream DNA. (A) The downstream
duplex is rotated by 30° toward the N-terminal domain
compared to its position in the elongation complex (shown in
gray). (B) The angle between the upstream and downstream duplex
DNA is about 40°, bringing the phosphate backbones within 6
Å of each other. (C) The refolded subdomain H from the
structure of the elongation complex (gray) creates a clash with
the position of the downstream DNA as observed in the
intermediate complex. Residues involved in the clash are shown
as spheres. (D) A close-up view of the 5' end of the 7-nt RNA
reveals that a modeled extension of the RNA by three additional
nucleotides would clash with the specificity loop in the
position observed in the intermediate complex.
|
