The TATA box binding protein (TBP2) from Arabidopsis thaliana has a form like a saddle. The folding topology is a symmetric alpha/beta structure containing two domains of 89-90 amino acids. Additionally there is a N-terminal segment of 18 amino acids (only a few are visible because of their large flexibility) . The carboxy terminl domains are phylogenetically conserved. They are built from a five-stranded antiparallel sheet and two helices each . The order of the strands in the sheet is S1 (24-33) - S5 (78-84) - S4 (69-73) - S3 (60-64) and S2 (50-53, in the ternary complex not recognizable as such) (in the other domain the structural elements are termed S1' etc.). The eight beta strands in the center comprise the concave lower side of the saddle , whereas the convex upper side is built from four helices and the basic connecting peptide (red) and the non-conserved amino terminus .
Like in many alpha/beta proteins there are numerous hydrophobic contacts between the alpha helices and the beta sheet. This part forms the hydrophobic body of the protein. Helix 1 touches parts of strands 2 and 3 . Helix 2 is on top of the pleated sheet and is in contact with strands S4, S5 and S1.
Near the C-terminus of TBP there are nine conserved prolines, some of which have an important function for the structure of the protein. Pro⁶⁷ (in the other domain Pro¹⁵⁸) features a cis-conformation and stabilizes a turn between beta-strands S3 and S4 (use the mouse to turn the molecule! You will detect Pro¹⁵⁸ between S3' and S4').
A special case is Pro¹⁹⁰ in helix 2'. In this position the axis of the helix is diverted, so the carboxy terminus is bent towards helix 1' . This item is the only significant difference between the domains of TBP. Pro¹⁹⁰ is phylogenetically conserved, so this feature is functionally important.
The corboxy terminus is additionally fixed to helix 1' by hydrogen bonds between Phe¹⁹⁵ and Lys¹²⁹ as well as between Arg¹⁹⁷ and Pro¹²⁷ .
The arms protruding down from the floor of the saddle are no flexible loops but stabilized by hydrophobic forces and hydrogen bonds. In additio there is a salt bridge between Glu⁵¹ and Arg⁵⁶ .

The peptide connecting the domains is basic because of two lysines contained therein . Overall the electric charge of the surface of the protein is distributed asymmetrically. There are 10 Arg, 20 Lys, 8 Asp and 11 Glu yielding a net charge of +11. Besides Glu¹⁸⁶ all charged amino acids are found at the surface of the protein (red = negative charge, blue = positive). Positive charges prevail in the 'left' part of the molecule.

TBP2 recognizes DNA in an 'induced fit' mechanism at a position with a TATA-Box . The protein binds to the minor groove of the DNA widening the groove in this spot. This induces a bend in the DNA. Between the amino acids of TBP and the TATA-box nucleobases there are numerous contacts involving all of the floor of the saddle .

To the complex of TBP and DNA binds the transcription factor TFII . TFII is aligned about parallel to the DNA . To elucidate the structure of this complex only the C-terminal part of TFII was used (amino acids 113-316). This part contains two similar domains which are connected by a short peptide . The structure of the domains is dominated by five helices . The other domain contains additionally two 3₁₀ helices . The domains are twisted towards each other by ca. 90º.

TFII is bound to TBP mainly by contacts to the loop emerging at the carboxy terminus from TBP . There are salt bridges (Aa red), hydrogen bonds (Aa cyan) and van der Waals-contacts (Aa yellow) (use your mouse to imagine all interactions). . There are more connections from TBP-helix 1' and the carboxyl terminus . TFII also contacts phosphate residues in the DNA beneath and in the TATA box .

this demonstration.

Literatur:
DB Nikolov & SK Burley, Nature Struct. Biol. 1 (1994) 621-637
DB Nikolov et al, Nature 377 (1995) 119-128