The TBP/TATA Box Complex

If Rasmol is not installed on this computer you will need to download Rasmol software

Click here to see TBP. You are now viewing the C-terminal domain of human TBP bound to the TATA box. This domain consists of two tandem copies of an approximately 90 amino acid sequence (one is shown in red, the other in blue). Each 90 amino acid sequence folds into a globular subdomain containing a five-stranded beta sheet and two alpha helices. Select the Cartoons command from the display menu to view the secondary structure. The two subdomains are related by a dyad axis. Note the symmetry of the structure.

The overall shape of TBP is that of a saddle. In each subdomain, a loop between a pair of antiparallel beta strands forms a "stirrup". The saddle sits atop the DNA. The beta sheets form the concave surface of the saddle and make extensive contact with the minor groove of the DNA. By entering the following series of commands into the command line window you will restrict the view to the DNA and the beta sheets and then convert the beta sheets to a spacefilling view. This should allow you to appreciate the beautiful fit between the DNA and the beta sheets.

restrict sheets or DNA

select sheets

spacefill on

color cpk

Click here to return to the original view. The fit between the protein and the DNA is clearly an "induced fit", since the structure of the DNA is severly distorted in the complex. Restrict the view to the DNA (enter the command restrict DNA). Then by translating and rotating the DNA molecule see if you can gain an appreciation for the nature of the distortion.

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