Mutation analysis by homology modeling of the NR2E3 homodimer DNA-binding complex. Amino acids 47–123 of human NR2E3 (SwissProt Acc. No. Q9Y5X4) were used for homology modelling on the SWISS-MODEL server with DeepView program (http://swissmodel.expasy.org) [30]–[32]. Crystallographic data of COUP-TF DBD (PDB Acc. No. 2EBL), RXR homodimer on DR1 DNA sequence (PDB Acc. No. 1BY4) and RXR/RAR heterodimer on DR1 DNA sequence (PDB Acc. No. 1DSZ) were used as templates. Secondary structures of the NR2E3 DBD monomer are shown as ribbons, i.e. starting from the N-terminus, 2 β-sheets of the first Cys4 zinc finger in green-yellow, the α-helix located in C-terminus of the first Cys4 zinc finger in yellow, the second α-helix located in C-terminus of the second Cys4 zinc finger in orange and the C-terminal α-helix of the T/A box in red (see also supplemental Figure 4). Residues p.R76 (left panels) and p.R104 (right panels) are shown with sidechains. For the DNA double helix all side chains are shown. Zinc ions are shown as small grey spheres. Residue p.R76 (left, upper panel) is located at the very C-terminus of the α-helix located in C-terminus of the first Cys4 zinc finger and directly contacts DNA through two hydrogen bonds (green dotted line). Both p.R76Q and p.R76W mutations disrupt hydrogen bond formation (left, middle and lower panels). The most favoured rotamers of the mutated residues all point towards the C-terminal a-helix of the T/A box. The bulky hydrophobic Trp sidechain might therefore impede dimerization. Residue p.104 (right, upper panel) is located in the middle of the α-helix located in C-terminus of the second Cys4 zinc finger. The sidechain points towards the inside of the protein, also in presence of the p.R104Q and p.R104W mutations (left, middle and lower panels).
http://plosone.org/article/info:doi/10.1371/journal.pone.0007379#article1.body1.sec5.supplementary-material8.caption1.p1

Some of the symbols in legend s8 do not appear. The correct legend should read: Mutation analysis by homology modeling of the NR2E3 homodimer DNA-binding complex. Amino acids 47-123 of human NR2E3 (SwissProt Acc. No. Q9Y5X4) were used for homology modelling on the SWISS-MODEL server with DeepView program (http://swissmodel.expasy.org) [30-32]. Crystallographic data of COUP-TF DBD (PDB Acc. No. 2EBL), RXR homodimer on DR1 DNA sequence (PDB Acc. No. 1BY4) and RXR/RAR heterodimer on DR1 DNA sequence (PDB Acc. No. 1DSZ) were used as templates. Secondary structures of the NR2E3 DBD monomer are shown as ribbons, i.e. starting from the N-terminus, 2 β-sheets of the first Cys4 zinc finger in green-yellow, the α-helix located in C-terminus of the first Cys4 zinc finger in yellow, the second α-helix located in C-terminus of the second Cys4 zinc finger in orange and the C-terminal α-helix of the T/A box in red (see also supplemental Figure 4). Residues p.R76 (left panels) and p.R104 (right panels) are shown with sidechains. For the DNA double helix all side chains are shown. Zinc ions are shown as small grey spheres. Residue p.R76 (left, upper panel) is located at the very C-terminus of the α-helix located in C-terminus of the first Cys4 zinc finger and directly contacts DNA through two hydrogen bonds (green dotted line). Both p.R76Q and p.R76W mutations disrupt hydrogen bond formation (left, middle and lower panels). The most favoured rotamers of the mutated residues all point towards the C-terminal a-helix of the T/A box. The bulky hydrophobic Trp sidechain might therefore impede dimerization. Residue p.104 (right, upper panel) is located in the middle of the α-helix located in C-terminus of the second Cys4 zinc finger. The sidechain points towards the inside of the protein, also in presence of the p.R104Q and p.R104W mutations (left, middle and lower panels).