Figure 5 - full size

 

Figure 5.
Figure 5. A Model of the Open ComplexT and NT strands are in magenta and cyan, respectively. (A) Overall stereo view. RNAP is represented by the surface of the electrostatic potentials, as in Figure 3A. ppGpp is blue. σND1 and σND2 are the two N-terminal σ subunit domains. Tyr β′1093 (yellow) stacks on the dwDNA T base at the entrance of the active site. (B) Enlarged stereo view of the open complex in the vicinity of the active and ppGpp binding sites. ppGpp (blue) in the 3′ orientation forms a putative base pair (red dashes) with the NT cytosine.

The above figure is reprinted by permission from Cell Press: Cell (2004, 117, 299-310) copyright 2004.