X-ray structures of TATA-binding protein (TBP). (a) A ribbon diagram of yeast TBP in the absence of DNA, in which α helices are red, β strands are yellow, and the remainder of the polypeptide backbone is cyan. The protein's pseudo-2-fold axis of symmetry is vertical. Note that the protein seems to be precisely the proper size and shape to sit astride a 20-Å-diameter cylinder of B-DNA. This, however, is not the case. [Based on an X-ray structure by Roger Kornberg, Stanford University. PDBid 1TBP.] (b) The structure of human TBP in complex with a 16-bp TATA box–containing duplex DNA (sense strand sequence CTGCTATAAAAGGCTG, with its TATA box in bold) viewed as in Part a. The DNA, which is largely in the B form, is drawn in stick form and colored according to atom type with sense strand C green, antisense strand C cyan, N blue, O red, and P orange. In the initial view, the DNA enters its binding site from behind with the 5 ′ end of the sense strand below the saddle on the right and exits toward the front to the left. The protein is drawn in worm form colored in rainbow order from its N-terminus (blue) to its C-terminus (red). The side chains of Phe residues 193, 210. 284, and 301, which induce sharp kinks in the DNA are drawn in stick form (magenta). Between the kinks, which are located at each end of the TATA box, the DNA is partially unwound with the protein's central 8 strands of its 10-stranded antiparallel β sheet inserted into and tracked along the DNA's greatly widened minor groove. The TBP does not contact the DNA's major groove. [Based on an X-ray structure by Stephen Burley, Structural GenomiX, Inc., San Diego, California. PDBid 1CDW.]