Structural Elements of an Orphan Nuclear Receptor–DNA Complex Qiang Zhao, Sepideh Khorasanizadeh, Yoji Miyoshi, Mitchell A. Lazar, Fraydoon Rastinejad  Molecular Cell  Volume 1, Issue 6, Pages 849-861 (May 1998) DOI: 10.1016/S1097-2765(00)80084-2

Figure 1 The Protein and DNA Constructs Used in Crystallization and Their Contacts (a and b) The upstream (a) and downstream (b) positioned DNA-binding regions of human RevErbα are numbered starting with the first conserved cysteine. The authentic numbers appear in the parentheses. Dashed lines indicate amino- and carboxy-terminal residues not found in the electron density maps. Closed and open arrows indicate direct and water-mediated hydrogen bonds to the DNA bases, respectively. Closed and open boxes indicate direct and water-mediated hydrogen bonds to the DNA phosphates. Colored circles indicate Van der Waals contacts with the DNA, and closed black circles indicate residues that mediate subunit dimerization. A symbol indicates one or more such contacts. (c) The 20 base pair DNA is numbered from the 5′ end, with arrows indicating the half-site repeats and boxes indicating the spacer and 5′ flanking sequence. Shown are the upstream (green) and downstream (red) contacts from the RevErb subunits. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 3 Minor Groove Contacts and Dimeric Assembly (A) Stereo diagram showing the interactions of the Grip-box residues 72–75 of the downstream subunit along the DNA minor groove. The DNA half-sites are blue, the spacer is white, and water molecules are pink. Hydrogen bonds and Van der Waals contacts are shown by white and red dotted lines, respectively. Residue 73 (Phe) is shown in yellow and varies among the class-I, -II, and -III receptors of Figure 5. The DNA numbers correspond to those in Figure 1c. (B) Stereo diagram of a portion of the 2|fo − fc| electron density map, showing the intersubunit dimerization contacts. Residues in green and red are from the upstream and downstream subunits, respectively. Dotted white and yellow lines indicate hydrogen bonds and Van der Waals interactions, respectively. The plus signs indicate water molecules. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 3 Minor Groove Contacts and Dimeric Assembly (A) Stereo diagram showing the interactions of the Grip-box residues 72–75 of the downstream subunit along the DNA minor groove. The DNA half-sites are blue, the spacer is white, and water molecules are pink. Hydrogen bonds and Van der Waals contacts are shown by white and red dotted lines, respectively. Residue 73 (Phe) is shown in yellow and varies among the class-I, -II, and -III receptors of Figure 5. The DNA numbers correspond to those in Figure 1c. (B) Stereo diagram of a portion of the 2|fo − fc| electron density map, showing the intersubunit dimerization contacts. Residues in green and red are from the upstream and downstream subunits, respectively. Dotted white and yellow lines indicate hydrogen bonds and Van der Waals interactions, respectively. The plus signs indicate water molecules. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 5 CTE Sequence Alignment of Homologous Orphan Receptors Showing Their Expected Minor-Groove Interfaces Minor-groove interfaces are highlighted. The receptors are divided into type-I, type-II, and type-III, depending on the length of their pre-Grip sequences and the sequence within the four-residue highlighted region. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 2 Overall Architecture of the Complex (a) The overall architecture of the complex. The green polypeptide and the red polypeptides are the upstream and downstream subunits, respectively. Zincs are shown as gray spheres. The conserved AGGTCA half-sites are shown in purple, and the 5′ flanking base pairs and spacer are shown in yellow. (b) Surface representation of the protein–DNA complex. The view is nearly identical to that shown in (a). The location of the Grip box in the minor groove is indicated. (c) Stereo diagram of the overall complex, showing the side chains (in yellow) mediating direct protein–DNA contacts and those coordinating the zinc ions (in pink). The green polypeptide is the upstream subunit. The yellow spheres are zincs, and their coordinating cysteines are in pink. The numbers along the DNA indicate the sequence as shown in Figure 1c. Half-Site Contacts (d and e) Schematic summary of upstream (d) and downstream (e) contacts between the core DBD and the half-sites. Red arrows indicate hydrogen bonding to the DNA phosphates; black arrows indicate other hydrogen bonds. The arrowhead indicates the probable hydrogen-bond acceptor. The contacts involve the side chains, unless otherwise stated. Amino acids in black make at least one direct hydrogen bond to the DNA bases. Residues circled in green make different DNA interactions in the two subunits. The blue circles are water molecules that mediate protein–DNA contacts. The yellow base pairs are different in steroid-receptor response elements. The DNA shown is underwound for clarity. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 2 Overall Architecture of the Complex (a) The overall architecture of the complex. The green polypeptide and the red polypeptides are the upstream and downstream subunits, respectively. Zincs are shown as gray spheres. The conserved AGGTCA half-sites are shown in purple, and the 5′ flanking base pairs and spacer are shown in yellow. (b) Surface representation of the protein–DNA complex. The view is nearly identical to that shown in (a). The location of the Grip box in the minor groove is indicated. (c) Stereo diagram of the overall complex, showing the side chains (in yellow) mediating direct protein–DNA contacts and those coordinating the zinc ions (in pink). The green polypeptide is the upstream subunit. The yellow spheres are zincs, and their coordinating cysteines are in pink. The numbers along the DNA indicate the sequence as shown in Figure 1c. Half-Site Contacts (d and e) Schematic summary of upstream (d) and downstream (e) contacts between the core DBD and the half-sites. Red arrows indicate hydrogen bonding to the DNA phosphates; black arrows indicate other hydrogen bonds. The arrowhead indicates the probable hydrogen-bond acceptor. The contacts involve the side chains, unless otherwise stated. Amino acids in black make at least one direct hydrogen bond to the DNA bases. Residues circled in green make different DNA interactions in the two subunits. The blue circles are water molecules that mediate protein–DNA contacts. The yellow base pairs are different in steroid-receptor response elements. The DNA shown is underwound for clarity. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 2 Overall Architecture of the Complex (a) The overall architecture of the complex. The green polypeptide and the red polypeptides are the upstream and downstream subunits, respectively. Zincs are shown as gray spheres. The conserved AGGTCA half-sites are shown in purple, and the 5′ flanking base pairs and spacer are shown in yellow. (b) Surface representation of the protein–DNA complex. The view is nearly identical to that shown in (a). The location of the Grip box in the minor groove is indicated. (c) Stereo diagram of the overall complex, showing the side chains (in yellow) mediating direct protein–DNA contacts and those coordinating the zinc ions (in pink). The green polypeptide is the upstream subunit. The yellow spheres are zincs, and their coordinating cysteines are in pink. The numbers along the DNA indicate the sequence as shown in Figure 1c. Half-Site Contacts (d and e) Schematic summary of upstream (d) and downstream (e) contacts between the core DBD and the half-sites. Red arrows indicate hydrogen bonding to the DNA phosphates; black arrows indicate other hydrogen bonds. The arrowhead indicates the probable hydrogen-bond acceptor. The contacts involve the side chains, unless otherwise stated. Amino acids in black make at least one direct hydrogen bond to the DNA bases. Residues circled in green make different DNA interactions in the two subunits. The blue circles are water molecules that mediate protein–DNA contacts. The yellow base pairs are different in steroid-receptor response elements. The DNA shown is underwound for clarity. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 2 Overall Architecture of the Complex (a) The overall architecture of the complex. The green polypeptide and the red polypeptides are the upstream and downstream subunits, respectively. Zincs are shown as gray spheres. The conserved AGGTCA half-sites are shown in purple, and the 5′ flanking base pairs and spacer are shown in yellow. (b) Surface representation of the protein–DNA complex. The view is nearly identical to that shown in (a). The location of the Grip box in the minor groove is indicated. (c) Stereo diagram of the overall complex, showing the side chains (in yellow) mediating direct protein–DNA contacts and those coordinating the zinc ions (in pink). The green polypeptide is the upstream subunit. The yellow spheres are zincs, and their coordinating cysteines are in pink. The numbers along the DNA indicate the sequence as shown in Figure 1c. Half-Site Contacts (d and e) Schematic summary of upstream (d) and downstream (e) contacts between the core DBD and the half-sites. Red arrows indicate hydrogen bonding to the DNA phosphates; black arrows indicate other hydrogen bonds. The arrowhead indicates the probable hydrogen-bond acceptor. The contacts involve the side chains, unless otherwise stated. Amino acids in black make at least one direct hydrogen bond to the DNA bases. Residues circled in green make different DNA interactions in the two subunits. The blue circles are water molecules that mediate protein–DNA contacts. The yellow base pairs are different in steroid-receptor response elements. The DNA shown is underwound for clarity. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 4 Comparison of Grip-Box Interactions (A) The crystallographically observed position of Grip-box residues of RevErb on DNA. The blue and white base pairs are half-site and flanking sequences, respectively. The yellow residue differs in the three classes of orphan receptors shown in Figure 5. The white ribbon shows the backbone trace of the CTE loop. (B and C) The expected conformation of the NGFI-B/NUR77 (B) and SF-1 (C) Grip boxes on their respective cognate sequences. (D) Comparison of the RevErb DBD (red) and the TR-DBD, showing the similarity along the 66-residue conserved core DBD and the different CTE folds. The white base pairs indicate sequences preceding the half-site of the Rev-DR2. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 4 Comparison of Grip-Box Interactions (A) The crystallographically observed position of Grip-box residues of RevErb on DNA. The blue and white base pairs are half-site and flanking sequences, respectively. The yellow residue differs in the three classes of orphan receptors shown in Figure 5. The white ribbon shows the backbone trace of the CTE loop. (B and C) The expected conformation of the NGFI-B/NUR77 (B) and SF-1 (C) Grip boxes on their respective cognate sequences. (D) Comparison of the RevErb DBD (red) and the TR-DBD, showing the similarity along the 66-residue conserved core DBD and the different CTE folds. The white base pairs indicate sequences preceding the half-site of the Rev-DR2. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 4 Comparison of Grip-Box Interactions (A) The crystallographically observed position of Grip-box residues of RevErb on DNA. The blue and white base pairs are half-site and flanking sequences, respectively. The yellow residue differs in the three classes of orphan receptors shown in Figure 5. The white ribbon shows the backbone trace of the CTE loop. (B and C) The expected conformation of the NGFI-B/NUR77 (B) and SF-1 (C) Grip boxes on their respective cognate sequences. (D) Comparison of the RevErb DBD (red) and the TR-DBD, showing the similarity along the 66-residue conserved core DBD and the different CTE folds. The white base pairs indicate sequences preceding the half-site of the Rev-DR2. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 4 Comparison of Grip-Box Interactions (A) The crystallographically observed position of Grip-box residues of RevErb on DNA. The blue and white base pairs are half-site and flanking sequences, respectively. The yellow residue differs in the three classes of orphan receptors shown in Figure 5. The white ribbon shows the backbone trace of the CTE loop. (B and C) The expected conformation of the NGFI-B/NUR77 (B) and SF-1 (C) Grip boxes on their respective cognate sequences. (D) Comparison of the RevErb DBD (red) and the TR-DBD, showing the similarity along the 66-residue conserved core DBD and the different CTE folds. The white base pairs indicate sequences preceding the half-site of the Rev-DR2. Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 6 Mechanism of Spacer Discrimination (A) The RevErb homodimer modeled on DR3, DR4, and DR5 response elements, with the spacer shown in yellow. In all three cases, the CTE region of the downstream subunit makes steric clashes (shown by [X]) with the Zn-II region of the upstream subunit, preventing coassembly. (B) Expected role of NGFI-B's 5′ flanking sequence in NGFI-B/RXR binding to DR1–DR5. RXR is shown in red, NGFI-B in purple, and the spacer DNA in yellow. Steric clashes between the subunits occur on all elements except the DR5. (C) Electrophoretic mobility shift assay showing the binding of PPAR/RXR on RevDR1, RevDR2, and the classical DR2 site (without RevRE-consensus flanking upstream half-site). Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 6 Mechanism of Spacer Discrimination (A) The RevErb homodimer modeled on DR3, DR4, and DR5 response elements, with the spacer shown in yellow. In all three cases, the CTE region of the downstream subunit makes steric clashes (shown by [X]) with the Zn-II region of the upstream subunit, preventing coassembly. (B) Expected role of NGFI-B's 5′ flanking sequence in NGFI-B/RXR binding to DR1–DR5. RXR is shown in red, NGFI-B in purple, and the spacer DNA in yellow. Steric clashes between the subunits occur on all elements except the DR5. (C) Electrophoretic mobility shift assay showing the binding of PPAR/RXR on RevDR1, RevDR2, and the classical DR2 site (without RevRE-consensus flanking upstream half-site). Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)

Figure 6 Mechanism of Spacer Discrimination (A) The RevErb homodimer modeled on DR3, DR4, and DR5 response elements, with the spacer shown in yellow. In all three cases, the CTE region of the downstream subunit makes steric clashes (shown by [X]) with the Zn-II region of the upstream subunit, preventing coassembly. (B) Expected role of NGFI-B's 5′ flanking sequence in NGFI-B/RXR binding to DR1–DR5. RXR is shown in red, NGFI-B in purple, and the spacer DNA in yellow. Steric clashes between the subunits occur on all elements except the DR5. (C) Electrophoretic mobility shift assay showing the binding of PPAR/RXR on RevDR1, RevDR2, and the classical DR2 site (without RevRE-consensus flanking upstream half-site). Molecular Cell 1998 1, 849-861DOI: (10.1016/S1097-2765(00)80084-2)