Nuclear receptor structure is composed of 5 domains:

A/B: N-terminal regulatory domain contains activation function 1 (residues 101-370), activation function 5 (residues 360-485) and dimerization surface (residues 1-36 and 370-494).

C: DNA binding domain (DBD)
D: Hinge region between DBD and LBD
E: Ligand binding domain (LBD) containing an which binds intramolecularly the N-terminal FXXFL motif or coactivators with the same motif (Human androgen receptor ligand-binding domain complex with modulator; PDB code 3b5r).^[1] Water molecules are shown as red spheres.
F: C-terminal domain

See also Receptor

Thyroid Hormone Receptor-like

Thyroid hormone receptor

• Thyroid hormone receptor

The .

Retinoic acid receptor

• Retinoic acid receptor

The .

• RA Mediated T-reg Differentiation; Retinoic acid acts as the ligand for the Retinoic Acid Receptor-α (RARα) / Retinoid X Receptor-α (RXRα) heterodimer

(PDB entry 1dkf). The Ligand binding domain for each piece of the dimer has a nearly identical structure of an . These α-helices form 12 domains per protein (H1-12), with an additional 2 β-sheets. The α-helical sandwich bind All-Trans Retinoic Acid (ATRA), the isomer of RA used by the body. Both monomers contain two regions of activity, the and the .

When RARα/RXRα proteins form a heterodimer, the overall structure of the larger dimer is comparable to that of an RXRα homodimer, likely due to the many similarities these 2 molecules share. RARα and RXRα rely on residues from the H7-10, L8-9, and L9-10 domains of both molecules to form the . The sequence identity between the 2 molecules on the dimer interface is 0.33.

The residues of α that are interacting in the heterodimer:

Hydrophobic residues: L356, F374, P375, L378, M379, I381 and A389 (yellow); Negatively charged residues: D338, D349, E353, E357, D383, and E393 (red); Positively charged residues: K360, R364, H372, K376, K380, and R385 (blue); Hydrophilic residues: Q315, Q352, T382, and S386 (green).

The residues of α that are interacting in the heterodimer are as follows:

Hydrophobic residues: Y402, P417, F420, A421, L424, L425, L427, P428, A429, and L435 (yellow); Negatively charged residues: E357, D384, E395, E399, E406, and E439 (red); Positively charged residues: R353, K361, R398, K410, K422, R426, R431, and K436 (blue); Hydrophilic residues: S432 (green).

Upon binding of the ligand ATRA in the cytoplasm, RARα and RXRα form a heterodimer and alter the C-terminals on domain H12 of both subunits in a manner that allows them to change the conformation of their DNA binding domains. The 2 proteins have 29% identity in their . For the ligand used in RARα crystallization, BMS614, 21 primarily hydrophobic residues form the . BMS614 is not the natural ligand for this molecule, but acts as stable agonist for crystallization. The largest difference between BMS614 and ATRA upon binding to the pocket are at Ile412, where BMS614 pushes much closer to the amino acid than ATRA does. Residues that form the binding pocket are found on H1, H3, H5, H11, L6-7, and L11-12 on RARα. The between RARα, RARβ and RARγ are present in this area: Residue 270: α:Ile β:Ile γ:Met; Residue 232: α:Ser β:Ala γ:Ala; Residue 395: α:Val β:Val γ:Ala

The is comprised of 16 primarily hydrophobic residues, found on the H3, H5, H7, H11, and L11-12 domains. The ligand used in the crystal, Oleic Acid, is similar to RA, and RA is capable of binding to the RXRα pocket.

(1by4).

When RXRα homodimers assemble on DNA, they form a 4 poplypeptide complex assembled via head to tail interactions along DR-1 repeated sequences. The structures of the polypeptides sit in the major grooves of the DNA chain, allowing for interaction with specific bases, giving a sequence specificity for the protein. The 2 do not alter their configuration upon DNA binding, but are used to guide the DNA into the correct position. Upon binding to DNA, the C-terminal end of the protein, referred to as the alters its conformation from α-helical to an extended conformation. This extended conformation allows Glu74 to move away from the DNA binding pocket and moves it so it interacts with the Zn(II) domain of the next polypeptide.

RXRα homodimers preferentially assemble on DR-1 repeat sequences. DR-1 sequences are composed of an AGGTCA tandem repeat, with a single nucleotide spacer in between the repeats. Only Lys22, Lys26, Glu19 and Arg27 interact with the DNA bases directly. interact with the phosphate backbone of the DNA molecule, making sure it is in position for base recognition. RXRα homodimers should to assemble on DR-2 tandem repeats, sequences with the same organization as DR-1, but with 2 nucleotides as a spacer. The DNA interaction is similar with DR-2 repeats, just spaced further apart.

Peroxisome Proliferator-Activated Receptors

PPARγ

• PPAR-gamma

Peroxisome proliferator-activated receptor γ (γ) is a protein in the nuclear receptors subfamily. It is 1 of 3 isotypes (-α, -β/ δ, and -γ) of PPAR receptors and has 2 protein isoforms governed by splice variations, which result in differences in the length of the N-terminal region (PPARγ1 and PPARγ2). PPARγ is involved in transcriptional regulation of glucose and lipid homeostasis, and helps regulate adipocyte differentiation. It has a , which allows it to interact with a wide array of ligands. triggers a conformational change of PPARγ, in the activation function-2 , which aids in the recruitment of co-regulatory factors to regulate gene transcription. PPARγ can form a with retinoic X receptor α (RXRα), a process necessary for most PPARγ-DNA interactions. PPARγ is a molecular target for antidiabetic drugs such as thiazolidinediones (TZDs), which makes the protein a target for Type II Diabetes (T2D) drug research.

PPARγ is composed of the ligand-independent activation domain (AF-1 region and A/B-domain), a DNA-binding domain (DBD) (C-domain), a hinge region (D-domain), and a ligand-dependent ligand-binding domain (LBD) (E/F-domain and AF-2 region). The 2 PPARγ isoforms, PPARγ1 and PPARγ2, differ by only 30 amino acids at the N-terminal end. These added amino acids on PPARγ2 result in increased potency and adipose-selectivity, which makes this protein a key player of adipocyte differentiation. The is composed of 13 α-helices and 4 short β-strands. It has a T-shaped binding pocket with a volume of ~1440 Å3, which is larger than that of most nuclear receptors, allowing for interactions with a variety of ligands. The PPARγ LBD is folded into a helical sandwich to provide a binding site for ligands. It is located at the C-terminal end of PPARγ and is composed of ~ 250 amino acids. Activation by full agonists occurs through hydrogen bond interactions between the S289, H323, Y473, and H449 residues of the PPARγ-LBD and polar functional groups on the ligand which are typically carbonyl or carboxyl oxygen atoms. Agonist binding results in a conformational change of the LBD AF-2 region, which is necessary for coactivator recruitment. This change can either be dramatic or subtle, which leads to stabilization of a charge clamp between helices H3 and H12 to aid in associations with the LXXLL (L, leucine; X, any amino acid) motif of the coactivator. Ligand binding of PPARγ is regulated by communication between the N-terminal A/B domain, which is adjacent to the DBD, and the carboxyl-terminal LBD.

The of PPARγ is a groove created by hydrophobic residues of the H3, H3’, H4, and H12 helices. Stabilization of the AF-2 domain is important for coactivator interactions, and is achieved through ligand binding. Upon agonist binding, coactivators and other chromatin-remodeling cofactors, like histone deacetylases, are recruited and transcription is activated. Coactivators can be regulated at the transcriptional and post-transcriptional levels, as well as by protein-kinase cascades. PPARγ can actively silence genes it is bound to by recruiting a corepressor in the absence of a ligand. Once this occurs, an antagonist binds to stabilize the AF-2 region, preventing interactions with coactivators and activation of transcription. Corepressor binding creates a 3-turn α-helix corepressor motif important for preventing the AF-2 domain from assuming an active conformation. Common coactivators of PPARγ include CBP/p300, the SRC family, and TRAP220. Common corepressors include SMART, NCoR, and RIP140.

• Pioglitazone is a selective agonist for Peroxisome Proliferator-Activated Receptor Gamma

Liver X receptor-like

Liver X receptor

. LXR in the LXR/retinoic X receptor β heterodimer in a hydrophobic .

Bile acid receptor (Farnesoid X receptor)

of human FXR ligand-binding domain (deeppink) complex with non-steroidal agonist, nuclear receptor coactivator 1 peptide (cyan) and sulfate ions (3ruu).

Vitamin D receptor-like

Vitamin D receptor

is a transcription factor. Upon binding to vitamin D, VDR forms a heterodimer with retinoid-X receptor and binds to hormone response receptors on DNA causing gene expression. The (green) binds to receptors in its target cells, controlling the synthesis of many different proteins involved in Ca transport and utilization.

.

. VDR contains 2 domains: a , that binds to the hormone (grey) and that binds to DNA (green and blue are 2 same VDR structures). It pairs up with a similar protein, 9-cis retinoic acid receptor (RXR), and together they bind to the DNA, activating synthesis in some cases and repressing it in others. When is mutated it is replaced with a which results in an inhibition of transcriptional activation. When transcription is inhibited it results in p53 accumulation, which activates and promotes p53 translocation into mitochondria leading to apoptosis. is replaced with when mutated creating a negative charge. The negative charge at the residue inhibits DNA binding which cause a downregulation of VDR activity. VDR needs DNA binding in order for it to be activated which is only possible with a serine residue.

The vitamin D nuclear receptor is a ligand-dependent transcription factor that controls multiple biological responses such as cell proliferation, immune responses, and bone mineralization. Numerous 1 α,25(OH)(2)D(3) analogues, which exhibit low calcemic side effects and/or antitumoral properties, have been synthesized. It was shown that acts as a 1α,25(OH)(2)D(3) superagonist and exhibits both antiproliferative and prodifferentiating properties in vitro. Using this information and on the basis of the crystal structures of human VDR ligand binding domain (hVDR LBD) bound to 1α,25(OH)(2)D(3), 2α-methyl-1α,25(OH)(2)D(3), or 2a, a novel analogue, 2α-methyl-(20S,23S)-epoxymethano-1α,25-dihydroxyvitamin D(3) (4a) was designed, in order to increase its transactivation potency.

Pregnane X receptor

• When activated, PXR binds to the retinoid X receptor (RXR) and the formed heterodimer binds to hormone response elements on the DNA (see below).

which is used in testing tuberculosis.

Retinoid X Receptor-like

Retinoid X receptor

• Retinoid X receptor

. Hydrophobic, Polar. . The ligand-binding residues are conserved in the 3 classes of RXR.

• RA Mediated T-reg Differentiation; Retinoic acid acts as the ligand for the Retinoic Acid Receptor-α (RARα) / Retinoid X Receptor-α (RXRα) heterodimer

Estrogen Receptor-like

Estrogen receptor

• Estrogen receptor

of estrogen receptor α complexed with raloxifene and a corepressor peptide (morph was taken from Gallery of Morphs of the Yale Morph Server).

Structure of estradiol metal chelate and estrogen receptor complex: The basis for designing a new class of SERMs^[2].

Selective estrogen receptor modulators, such as estradiol 17-derived metal complexes, have been synthesized as targeted probes for the diagnosis and treatment of breast cancer. The detailed 3D structure of bound with a novel at 2.6Å resolution was reported (2yat). The residues with EPTA-Eu. The hydrogen bonds are shown as white dashed lines. of this structure with the structure of native ligand 17β-estradiol (E2) in the complex of E2/ERα-LBD complex (1ere) reveals that the . The made by additional estrogen receptor residues (e.g. Glu419 of H7 and Glu339 of H3, this depends on subunit), may work together with the E2 17β hydroxyl-His524 hydrogen bond and tighten the neck of the LBP upon binding of the endogenous ligand E2. 4-Hydroxytamoxifen (OHT) is an other selective estrogen receptor modulator. of EPTA-Eu/ERα-LBD complex on OHT/ERα-LBD complex (3ert) shows that there is similar network of hydrogen bonds in both complexes, except for His524 which does not form hydrogen bond with OHT in the OHT/ERα-LBD complex. E2/ERα-LBD (1ere), OHT/ERα-LBD (3ert) and EPTA-Eu/ERα-LBD shows that they overlap well in the majority portions of the domain, but differ significantly in the region of the 'omega loop'. They display different synergistic reciprocating movements, depending on the specific nature of the ligand bound. The structure of estrogen receptor complexed with EPTA-Eu provides important information pertinent to the design of novel functional ER targeted probes for clinical applications.

• Ivan Koutsopatriy estrogen receptor

ER is a modular protein composed of a ligand binding domain, a DNA binding domain and a transactivation domain. ER is a DNA-binding transcription factor.

. The DNA binding domain can be clearly observed in this scene; the highlighted yellow helix in close proximity to the DNA is part of the DNA binding domain. The blue beta sheet close to the yellow DNA binding alpha helix is also part of the DNA binding domain. The transactivation domain forms an alpha helix which is colored in purple. The transactivation domain activates RNA polymerase when the receptor binds to DNA. The ligand binding domain may be observed here with the following scene.

. The ligand ferutinine (highlighted in pink) is bound by the ligand binding domain, composed of the blue colored alpha helices immediately surrounding the purple ligand. Another view of the ligand binding domain is shown here, with estradiol bound. .

ER is functional as a ligand-dependent transcription factor. ER responds to both agonist and antagonist ligands and can associate with the nuclear matrix. Differences in the structure of the receptor are observed depending on what ligand ER has bound (if any). Through comparisons of ER bound to agonist and antagonist ligands, some structural components may be highlighted. The specific conformation of this tight loop of alpha helices and beta sheets around the ligand shows a complex capable of activating ER's transcription loci. This complex allows for the activation signal that will stimulate normal growth.

Normal growth is stimulated when an agonist bound ER binds DNA. This occurs with the assistance of chaperon proteins. These chaperons are capable of recognizing estrogen receptor ligand complexes. When ER has bound a ligand chaperons facilitate the trans-location of the complex to the nucleus. Eventually the chaperon ligand ER complex will reach specific euchromatin, at which point the chaperons facilitate the ligand ER complex to changes conformation. This conformation will facilitate the estrogen receptor to bind the DNA major groove at specific palindromic sequences. Estradiol is a normal ligand for ER and allows for binding in the major groove of DNA.

If the ligand is an antagonist the transcription factor function of estrogen receptor becomes hindered. The conformation of ER bound to the partial agonist genistein has a loop which is not as tight around the ligand as those found on ER with a complete agonist ligand. The ligands themselves take up different amounts of space and have varying interactions within ER. This slight difference effects the ability of the chaperon to be able to bind the receptor ligand complex to the major groove of DNA. There is a noticeable difference in the size of the pure agonist vs partial agonist scenes. Specifically, look at the width of the agonist compared to the partial agonist.

Similar differences may be observed between ER which has bound the partial agonist and complete antagonist ligands. The most drastic difference is noticeable between agonist and antagonist ligands. Compare the agonist scene to the . Special attention should be given to the bottom right alpha helices and beta sheets that are pushed out more in the antagonist compared to the agonist bound ER.

Estrogen receptor α

• Estrogen receptor#Estrogen receptor α complexed with raloxifene and a corepressor peptide

Estrogen receptor β

• Student Project 10 for UMass Chemistry 423 Spring 2015

(ER-β) is 1 of the 2 isoforms of the estrogen receptor, a ligand-activated transcription factor which regulates the biological effects of the steroid hormone 17 β-estradiol, or estrogen, in both males and females. The complex is a hetero-tetrameric assembly consisting of 4 molecules and a ligand: 2 copies of , 2 copies of , and the ligand, . Once the ligand is bound, the complex recruits the steroid receptor coactivators, which recruit other proteins to form the transcriptional complex for initiation of transcription. This activates expression of reporter genes containing estrogen response elements. Genistein is a phytoestrogen with structural similarity to estrogen which competes for estrogen receptors.

Although estrogen receptor β is widely expressed, it is not the primary estrogen receptor in most tissues. As a result, it has become a target for drug delivery, especially since it is 40x more selective for genistein than the α isoform. This enhanced selectivity may be caused by differences in residues between the 2 isoforms, allowing ER-β to accommodate more polar substituents in its binding pocket. ER-β differs greatly from ER-α at the N-terminal domains, which can be seen located at opposite ends from the C termini in this . The protein is composed of 3 sections: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.

Each ERβ contains several domains with specific functions: an N-terminal domain (NTD), a DNA-binding domain (DBD), a flexible hinge region and a C-terminal Ligand-binding domain (LBD). The complex overall is about . The is the 1st activation function (AF-1) domain that consists mostly of random coils and a small portion of helices (red) and sheets (green); it is a . This lack of structure allows the region to recruit and bond many different interaction partners. This region also has the capacity to transactivate transcription without binding estrogen.

The binds estrogen response elements (ERE) of target genes and recruits coactivator proteins responsible for the transcription of these genes. The ERE consist of a palindromic inverted repeat 5'GGTCAnnnTGACC-3' of target genes. The DBD is a highly . It is composed of 2 C4-type Zn fingers each containing residues coordinating to a Zn atom.

The hinge region connects the DBD and LBD.

binds estrogen, coregulatory proteins, corepressors and coactivators. Genistein is not generated by the endocrine system that binds ERβ like estrogen; both ligands are completely buried within the

(Hydrophobic, Polar) of the ERβ complex.

Binding at the LBD activates transcription mediated by the DBD. This domain is entirely helical; the LBD interacts with genistein through helices. The conformationally dynamic portion of this region gives rise to ERβ’s ligand-dependent transcriptional activation (AF-2) function. A key element of AF-2 is helix 12 (H12), which acts as a conformational switch; different receptor ligands influence the orientation of H12. Agonist ligands like genistein position H12 across the ligand-binding pocket of the LBD, which provides a coactivator docking surface. Geinstein binding allows the helices of AF-2 to form a shallow hydrophobic binding site for leucine-rich motifs of coactivators to bind. This conformation provides optimal interaction with coactivators and transcription is activated.

Genistein's bicyclic form allows it to hydrogen bond on opposite sides with the hydroxyls of the histidine groups on the receptor. binding to the receptor causes a conformational change and activates the receptor resulting in up-regulation for coactivators. Down-regulation will occur in the presence of corepressor as they bind to repressors and indirectly regulate gene expression. In order for the estrogen receptor β genistein to bind to a receptor and activate it there must be stabilization by a coactivator. The coactivator increases the gene expression and with this increase allows it to bind to an activator group consisting of a DNA binding domain. The estrogen receptor is found to be comprised of a dimer attached to a ligand and coactivator peptide which helps to stabilize the structure of each monomer. The conformational state of helix-12 can be modified by the binding of the coactivator.

This depicts the hydrophobic and hydrophilic residues of the estrogen receptor. The hydrophobic regions are primarily on the inside of the protein surrounding genistein (red). Having the hydrophobic residues surrounding the binding pocket will stabilize the structure. The structure of this pocket is tertiary and do to the hydrophobic interactions inside the pocket and hydrophilic interactions on the outside help to stabilize this tertiary structure. The is hydrophobic which means that an increase in lipophilicity would increase the affinity for ligands which in this case is genistein. The genistein structure has 3 hydroxyl groups, an ether and an ester. These 3 functional groups are polar and have many possibilities for hydrogen bonding. The His475 and Met336 residues in the binding pocket are capable of forming hydrogen bonds with genistein do to the many hydrogen bond forming functional groups. These residues are different from the residues found in ERα and so the selectivity of genistein is much greater for ERβ.

Upon visualizing the estrogen receptor in an , the structure can be classified as parallel or anti-parallel. Here is the zoomed .

Estrogen-related receptor

• • Tamoxifen and the Estrogen Receptor/Tamoxifen and the Estrogen-related receptor

to human estrogen-related receptor γ. The chemotherapeutic drugs bisphenol and are nestled between 4 alpha helices in the ERR active site.

3-Ketosteroid receptors

Glucocorticoid receptor

Mineralocorticoid receptor

The MR ligand aldosterone binds in a (Alpha Helices,  Beta Strands ,  Loops , Turns). ^[3]. . Water molecules are shown as red spheres.

Progesterone receptor

The structure of the complex of the ligand-binding domain of PR with RU486 - an abortion-inducing drug - shows the ligand bound at a similar location to other agonists or partial agonists with a flexible loop of PR being a possible entry route to the

Androgen receptor

AR structure is composed of 5 domains: A/B: N-terminal regulatory domain contains activation function 1 (residues 101-370), activation function 5 (residues 360-485) and dimerization surface (residues 1-36 and 370-494).

C: DNA binding domain (DBD)

D: Hinge region between DBD and LBD

E: Ligand binding domain (LBD) containing an which binds intramolecularly the N-terminal FXXFL motif or coactivators with the same motif.

F: C-terminal domain

Liver receptor homolog-1?

The .

.