Figure 2
From: Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor
(a) Overall structure of RXR DBD-Ramp2. The upstream RXR (in light cyan) and downstream RXR (in cyan) bound to their hexanucleotide motifs shown in red. The spheres indicate the Zn molecules. (b) Comparison of DNA bending of the DR1 elements. The ds oligonucleotides used in the crystallographic structures of RXR-DBD homodimers complexed with DR1, show similar deformation. (c) Plot of the minor groove widths of the DR1 ds oligonucleotides. The values were derived using the 3DNA software. The solid black line represents standard values for B-DNA. (d-e) RXR homodimers exhibit specific interactions and polarity on natural DR1s. Ramp2 DNA sequence recognition by the upstream RXR subunit (d). View along the DNA-recognition helix (α1) of RXR showing residues Glu153, Lys156, Arg161 and Arg209 and their direct and water-mediated base contacts. Hydrogen-bonds and water molecules are shown as dotted blue lines and dark spheres, respectively. The interspacer nucleotide is highlighted in grey. The corresponding view of Ramp2 DNA sequence recognition by the downstream RXR subunit (e).
