Harris et al. Figure 3

FIGURE 3 Computer models of the ER DBD from NMR structure determination with putative flanking alpha helices attached are shown docked at a 29bp sequence of VITA1 ERE1. A composite of amino acid and codon alignments from figure 3d below are highlighted on the protein and DNA respectively (figure 3a-c). All highlighted residues have a dot surface indicating the van der Waals surfaces of each atom in that residue. The DNA nucleotides are color coded: Ade = green, Thy = red, Gua = yellow and Cyt = blue. Color coding of amino acids is based on polarity: positively charged side chains = blue, negatively charged side chains = red, uncharged polar side chains = yellow and nonpolar side chains = purple. The protein is docked at a distance of about 10 angstroms from the DNA for visual clarity. Above the DNA models is a schematic of the DNA sequence. Boxes represent the ERE right and left DNA major groove halfsites.

Exon 2 encoded DNA recognition helix alignments.

Exon 3 encoded beta strand alignments.

Exon 4 encoded putative alpha helix alignments.

The nucleotide sequence of VITA1 ERE1 is translated to amino acids in Dayhoff (17) one-letter code for all reading frames on both strands. Circles, triangles and squares indicate codons in the DNA sequence with which cognate amino acids from the ER DBD are aligned. Circles = codons for exon 2 encoded DNA recognition helix amino acids, triangles = codons for exon 3 encoded beta strand amino acids and squares = codons for exon 4 encoded putative alpha helix amino acids. The amino acid sequences of these structures are shown at the bottom of the figure. Amino acids aligned with cognate codons are indicated with dots above.