Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes
Fig 5
MD relaxation of NTP in the main channel and the secondary channel.
(a-b) Initially, the points constituting the entry routes through the main and secondary channels were divided into 20 clusters. The yellow and orange spheres represent the center of each cluster for the main channel and the secondary channel, respectively. (c-d) A NTP molecule (in licorice presentation) accompanied by a bound magnesium atom (sphere representation) was aligned to each of the cluster centers (shown in (a-b)) by its center of mass (see Methods). These conformations were used as starting points for relaxation via MD simulations (see Methods). The template DNA, non-template DNA and mRNA strands are shown in cyan, green and red, respectively, with tube and licorice representations. The cut-view of the protein is shown in grey with a surface representation.