This is T7 RNA Polymerase in its elongation phase, complexed with DNA and RNA.
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to get a better glimpse of the nucleic acids within the polymerase structure.
In this view,
DNA can be seen entering the polymerase from the right side. As elongation progresses, RNA exits through a tunnel at the center of the complex.
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for a closer look at the tunnel. The presence of this structure contributes to the elongation complex's increased processivity.
Here,
a structure called the specificity loop is highlighted in red. During the initiaton phase, the specificity loop interacts in a sequence-specific manner with the promoter DNA. In the elongation phase, however, it shifts position and becomes part of the exit tunnel.
This view
highlights the intercalating hairpin (yellow). This structure opens the promoter during initiation, but becomes disordered and inactive during the elongation phase, as shown.
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to see several important structures within the polymerase. Helix Y (red) seperates the non-template DNA from template DNA. Residue 644 (Phe, magenta) interacts with the first base downstream from the transcription bubble. Subdomain H (yellow) stabilizes the non-template DNA.
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to view only the DNA and RNA. This view highlights the "transcription bubble." This structure is characterized by the seperation of the DNA heteroduplex, with RNA (yellow) annealed to the template DNA (light blue). From left to right, the non-template DNA (green) is running 5' to 3'.
Here,
the hydrogen bonds between the newly added RNA and template DNA are highlighted.
This view
shows the last RNA base that is annealed to the template DNA, as well as the 5' unbound transcript.
Can you guess how the protein is oriented now?
A-ha! We have another view of the 5' RNA leaving the exit tunnel.