FIGURE 4
A computer model of ER DBD dimer from x-ray crystallographic structural determination (PDB structure ID: 1HCQ) in complex with the 25 bp distal non-consensus ERE nucleotide sequence upstream of the Xenopus laevis vitellogenin A1 gene (GenBank locus XLVITA15). The protein is docked at a distance of about 10 angstroms from the DNA for visual clarity. Color coding for nucleotides and amino acids is as in figure 3. Amino acids of the ER DBD which are oriented toward the ERE are labelled using the Dayhoff one letter code (36) and are numbered as in the human ER (37). Above the DNA model is a schematic of the VITA1 ERE and flanking regions, numbered above and below with the 5' sense strand read left to right, starting at -377 upstream from the Xenopus laevis vitellogenin gene (GenBank locus XLVITA15) transcription start site and ending at -353 = 1 to 25. The antisense strand reads right to left from -353 to -377 = 26 to 50. The ER/ERE model shown is to be used as a key for locating interactions from molecular dynamics found between the ER DBD amino acids and nucleotides of the ERE and its flanks (see Table I). The color coding and numbering scheme in this figure is used in all subsequent molecular models.