Examples of chemical structures of RXR ligands. A. Natural products that act as RXR ligands: 9-cis-retinoic acid, (E)-5,8,11,14,17,20-docosahexaenoic acid, lithocholic acid, and phytanic acid. B. Synthetic RXR transcriptional agonists; 9cUAB30, AGN194204, CD3254, LG100268, LG101305, methoprene acid, PA024, SR11217, and SR11237 (BMS649). C. Synthetic RXR synergist: HX600. D. Synthetic RXR transcriptional antagonists: HX531, PA452, UVI3003, and XCT0135908.

RXRα protein domains and ligand-binding domain structure. A. Map of human RXRα functional domains. Adapted from Ref. []. B. Human RXRα ligand-binding domain (LBD) without a bound ligand as found in Protein Data Bank (PDB) crystal structure of the apo-RXRα LBD homodimer 1LBD. C. Human RXRα LBD complexed with transcriptional agonist SR11237 (BMS649, with carbon atoms in gray) as found in PDB crystal structure 1MVC. Protein backbones are shown in ribbon format.

Retinoid X Receptor (RXR) DNA-binding domain (DBD) interaction with DNA. A. Direct repeat (DR) sequence half-sites (5′-AGGTCA-3′) separated by X = 1–5 base-pairs (n) to which RXRα, β, and γ bind as an RXR homodimer or as an RXR heterodimer with retinoic acid receptor (RAR) subtypes 〈, β, and γ, peroxisome proliferator-activated receptors (PPARs) 〈, β/δ, and γ, chick ovalbumin uncoupled protein-transcription factor (COUP-TFs) I and II, vitamin D receptor (VDR), thyroid hormone receptor (TR), liver X receptors (LXRs) 〈 and β, nerve growth factor I beta (NGFI-B/TR3/Nur77) in which RXR is the upstream (5′) binding partner. n, undefined nucleotide base-pair that separates the direct repeats of 5′-AGGTCA-3′. Degenerate sequences also exist. B. Structure of the RXR〈 DBD showing the two zinc fingers (I and II), each of which is stabilized by complexation of a zinc(II) ion (shown in gold) with four of its cysteine sulfhydryl groups (zinc finger I: C135, C138, C152, and C155; and II: C171, C177, C187, and C190). Recognition helix (C152–R164) and helix II (C187–M198) α-helical sequences are shown in red and bracketed. The T-box sequence (K201–R209) is shown in blue. According to NMR studies, when the RXRα DBD monomer was free in solution, its T-box was helical with its E208 residue (magenta) interacting with K160 and R164 (cyan) of the recognition helix. However, according to the crystallographic structure of two RXR〈 DBD homodimers (1BY4), each of which was bound to a direct repeat sequence that was separated by one base-pair—DR-1 (n = A, X = 1) RXRE—that were separated by two residues giving rise to an internal DR-2 ((n)_X = GT, X = 2) RXRE, the T-box was a random coil that allowed the R164 side chain to interact with DNA and the K160 side chain to interact with DNA through a water molecule. As a result, the residues K156, E153, and R161 of the most upstream DBD interacted with the most upstream (5′) half-site of the first DR-1 nucleotides 5′-G₂, 3′-C₃, and 3′-G₅, respectively, and residues K22, E19, K26, and R27 of its downstream partner (second DBD) interacted with the downstream DR-1 half-site nucleotides of the first DR-1, namely 5′-G₉, 3′-C₁₁, 3′-G₁₂ (through water), and 3′-G₁₂ (directly and through a water), respectively. Interactions of the third RXR〈 DBD with the second DR-1 upstream half-site base-pairs were as follows: K160 with the 3′-C₃ and 3′-A₄ (both through a water), E153 with 3′-C₃, and R161 with 3′-G₅ (directly and through a water), and those of its downstream partner (fourth DBD) with the downstream half-site of the second DR-1 were: K156 with 5′- G₁₀ (through a water), K160 with 5′-G₁₀ (directly and through a water), G153 with 3′-C₁₀ (directly) and 3′-A₁₁ (through a water), and R161 with 3′-G₁₂. Thus, contacts of the four RXR〈 DBDs with the nucleotide bases varied and depended on their upstream or downstream position on each DR-1 and to which of the two DR-1 sites they bound. DBD residues R164, N185, R191, R161, and Q188 interacted with phosphate residues of the 5′-G₃, 3′-G₅, 3′-G₅, 3′-T₆, and 3′-T₆, respectively, whereas Q206 and K145 interacted with phosphates adjacent to 5′-G₂ and 5′-A₇ from an adjacent subunit, respectively. These residues are underlined. A, adenosine; C, cytosine; G, guanosine; and T, thymidine. Adapted from Ref. [].

Structure of the rosiglitazone–PPARγ–RXRα–9-cis-RA complex bound to two coactivator (CoA) NCoA2 peptides and DNA (PDB 3DZY). Components are colored as follows: PPARγ LBD (blue), DBD (cyan), ligand (carbons in orange), and CoA peptide (gray); RXRα LBD (magenta), DBD (red), ligand (Cs in yellow-green), and CoA peptide (pink); and DNA backbone (orange), nucleosides (blue and green). The RXRα LBD helices are numbered. Note that the RXRα hinge was not defined in 3DZY due to absence of electron density. Adapted from Ref. [].

RXRα ligand-binding domain (LBD) functional domains. A. Structure of RXRα LBD ligand-binding pocket showing contacts between pocket residues and RXR agonist SR11237 (BMS64) as found in the PDB structure 1MVC. Two views of the residues in helices H3 (backbone and residue side-chain Cs in blue), H5 (Cs in cyan), H7 (Cs in green), and H11 (Cs in orange) and β-sheet (Cs in gray) contacting SR11237 (Cs in magenta). B. RXRα LBD CoA surface residues (cyan backbone and residue side-chain Cs) forming salt-bridge contacts that stabilize binding of the CoA GRIP-1 peptide (rose) as shown in 1MVC. C. PPARγ LBD–RXRα LBD heterodimer interface as found in PDB 3DZY with RXRα residue contacts labeled. PPARγ and RXRα backbones and side-chain Cs in pink and cyan, respectively. Ns (blue), Os (red), and S (yellow). A, alanine; C, cysteine; D, aspartate; E, glutamate; F, phenylalanine; H, histidine; I, isoleucine; L, leucine; N, asparagine; Q, glutamine; R, arginine; V, valine; W, tryptophan; and Y, tyrosine.

Transcriptional activation by nonpermissive, permissive, and conditionally permissive heterodimers of RXR and another nuclear receptor (NR). A. Transcriptional activation by a nonpermissive heterodimeric partner such as thyroid hormone receptor (TR) or vitamin D receptor (VDR). The nonpermissive NR is dominant so that binding by its agonist (T₃ or VD₃) controls the recruitment of a coactivator protein (CoA) to the TR or VDR AF-2 surface of the RXR–TR or VDR complex bound to its response element (TRE or VDRE) in the promoter region of a T₃ or VD₃-activated gene. The bound CoA could then recruit a histone acetylase, a bridging or scaffolding protein, and the transcriptional complex to initiate gene transcription from the nonpermissive-ligand responsive gene transcriptional start site (TS). Binding of an RXR agonist would not enhance the response induced by the bound TR or VDR agonist. B. Transcriptional activation by a permissive RXR heterodimeric partner such as farnesoid (bile acid) X receptor (FXR), liver (oxysterol) X receptor (LXR), and peroxisome proliferator-activated receptor (PPAR). An agonist of either partner in the heterodimeric pair such as RXR–PPAR could bind its own NR to initiate the recruitment of a CoA to the RXR–NR (RXR–PPAR) complex bound to its NRE (PPRE) in the promoter region of an NR (PPAR) agonist-responsive gene. Thus, either agonist-bound RXR or NR (PPAR) could recruit a coactivator (CoA), a histone acetylase, a bridging or scaffolding protein, and the transcriptional complex to initiate gene transcription. Binding of an agonist to the second NR in the dimer would enhance the transcriptional response induced by first NR–agonist complex either additively or synergistically. C. Transcriptional activation by the conditionally permissive heterodimeric partner RAR. Binding of the RAR agonist would control the transcriptional response and also permit the binding of an RXR agonist. Thus, the RAR–agonist complex would be permissive. The RXR–agonist complex would then enhance the transcriptional response induced by the RAR agonist. Adapted from Refs. [] and [].

Cartoon demonstrating behavior of RXRα ligand-binding domain (LBD) helix H12 in the context of its homodimeric complex with bigelovin and coactivator (CoA) SRC-1 peptide (PDB structure 3OZJ), the apo-tetramer (1G1U), the tetramer bound with four corepressor (CoR) SMRT2 peptides (3R29), and the tetramer bound with two molecules of antagonist rhein and two CoR SMRT2 peptides (3R2A). In 3OZJ, H12 of each monomer formed an AF-2 surface with its H3 and H4 to bind the CoA peptide despite bigelovin demonstrating antagonist behavior by repressing wild-type RXRα basal transactivation activity in a reporter assay (Ref. []). In 1G1U, H12 of each monomer of the tetramer formed a surface with helices H3 and H4 of the monomer from the opposing homodimer to repress transactivation. In 3R29, H12 of each monomer formed a CoR surface with H3 and H4 of a monomer from the opposing dimer to bind one CoR peptide. In 3R2A, the homotetramer was composed of two homodimers, each containing one monomer bound with rhein and the other bound with a CoR peptide. The CoR surface of the monomer that bound the CoR peptide was composed of its own H3 and H4 with H12 from the monomer to which rhein was bound in the adjacent dimer. The backbones of each monomer differed as did the structures of the CoR peptides and the positions of the rhein ligands. The more ordered CoR peptide-bound monomer dimerized with the more disordered ligand-bound monomer and vice-versa. Cartoon based on Refs. [] and [].

Major differences occur in the human RXRα ligand-binding domain (LBD) structures when complexed as apo-tetramers and corepressor (CoR) peptide-bound tetramers compared to the agonist and antagonist-bound structures. A. Structure of one RXRα LBD monomer (light-pink backbone) complexed with transcriptional agonist 9-cis-RA (C atoms in brown) and coactivaor (CoA) GRIP-1 peptide (magenta backbone) (PDB 3OAP homodimeric LBD–9-cis-RA complex) of the superposed with that of one RXRα LBD monomer (cyan backbone) complexed with the antagonist rhein (Cs, blue) (PDB 3R2A tetrameric LBD complex containing two rhein molecules and two peptides). B. RXRα LBD monomer (green backbone) complexed with CoR SMRT2 peptide (yellow backbone) (PDB 3R29 tetrameric LBD–SMRT2 complex) superposed with one RXRα LBD monomer (cyan backbone) complexed with antagonist rhein (Cs, blue) (PDB 3R2A tetramer complex. C. RXRα LBD monomer (light-pink backbone) complexed with 9-cis-RA (Cs, brown) and GRIP-1 peptide (magenta backbone) (PDB 3OAP) superposed with one RXRα LBD monomer (green backbone) complexed with SMRT2 peptide (yellow backbone) (PDB 3R29 tetramer complex). RXRα LBD helices are numbered. Ligand Os in red.

Overlap of structures of human RXRα ligand-binding domains (LBDs) complexed with transcriptional antagonists that occupy the hydrophobic portion of the L-shaped RXRα ligand-binding pocket (LBP). View of the LBP (green backbone and residue side-chain Cs) in the more-ordered monomer bound with antagonist rhein (blue Cs) as found in the tetrameric LBD complex containing two molecules of rhein and two corepressor (CoR) SMRT2 peptides (PDB 3R2A). This view is overlaid with that of the LBP (magenta backbone and residue side-chain Cs) bound with bigelovin (orange Cs) as found in the homodimeric LBD complex with two coactivator (CoA) SRC-1 peptides (PDB 3OZJ). LBP residues within 4.0 Å of the ligand are shown. Helices H3, H5, H7, and H11 and their side chains having similar positions are labeled in black. Those side chains occupying different positions in the two structures are labeled according to their backbone colors. See H11 F439, for example. Although F349 is reported to have a major role in tetramerization, its position in 3OZJ appears not to support participation. The 1-OH and 8-OH O atoms of rhein were within 3–4 Å of the C432 backbone O (red bond above the H435 label), whereas similar H-bond stabilization for bigelovin was not observed. O atoms in red; Ns, blue; Ss, yellow.