Summary: Zinc finger, C4 type (two domains)
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Nuclear receptor Edit Wikipedia article
In the field of molecular biology, nuclear receptors are a class of proteins found within cells that are responsible for sensing steroid and thyroid hormones and certain other molecules. In response, these receptors work with other proteins to regulate the expression of specific genes, thereby controlling the development, homeostasis, and metabolism of the organism.
Nuclear receptors have the ability to directly bind to DNA and regulate the expression of adjacent genes, hence these receptors are classified as transcription factors. The regulation of gene expression by nuclear receptors generally only happens when a ligand â€” a molecule that affects the receptor's behavior â€” is present. More specifically, ligand binding to a nuclear receptor results in a conformational change in the receptor, which, in turn, activates the receptor, resulting in up-regulation or down-regulation of gene expression.
A unique property of nuclear receptors that differentiates them from other classes of receptors is their ability to directly interact with and control the expression of genomic DNA. As a consequence, nuclear receptors play key roles in both embryonic development and adult homeostasis. As discussed below, nuclear receptors may be classified according to either mechanism or homology.
- 1 Species distribution
- 2 Ligands
- 3 Structure
- 4 Mechanism of action
- 5 Coregulatory proteins
- 6 Agonism vs antagonism
- 7 Alternative mechanisms
- 8 Family members
- 9 History
- 10 See also
- 11 References
- 12 External links
Nuclear receptors are specific to metazoans (animals) and are not found in protists, algae, fungi, or plants. Amongst the early-branching animal lineages with sequenced genomes, two have been reported from the sponge Amphimedon queenslandica, two from the ctenophore Mnemiopsis leidyi four from the placozoan Trichoplax adhaerens and 17 from the cnidarian Nematostella vectensis. There are 270 nuclear receptors in the nematode C. elegans alone. Humans, mice, and rats have respectively 48, 49, and 47 nuclear receptors each.
Ligands that bind to and activate nuclear receptors include lipophilic substances such as endogenous hormones, vitamins A and D, and xenobiotic endocrine disruptors. Because the expression of a large number of genes is regulated by nuclear receptors, ligands that activate these receptors can have profound effects on the organism. Many of these regulated genes are associated with various diseases, which explains why the molecular targets of approximately 13% of U.S. Food and Drug Administration (FDA) approved drugs are nuclear receptors.
A number of nuclear receptors, referred to as orphan receptors, have no known (or at least generally agreed upon) endogenous ligands. Some of these receptors such as FXR, LXR, and PPAR bind a number of metabolic intermediates such as fatty acids, bile acids and/or sterols with relatively low affinity. These receptors hence may function as metabolic sensors. Other nuclear receptors, such as CAR and PXR appear to function as xenobiotic sensors up-regulating the expression of cytochrome P450 enzymes that metabolize these xenobiotics.
- (A-B) N-terminal regulatory domain: Contains the activation function 1 (AF-1) whose action is independent of the presence of ligand. The transcriptional activation of AF-1 is normally very weak, but it does synergize with AF-2 in the E-domain (see below) to produce a more robust upregulation of gene expression. The A-B domain is highly variable in sequence between various nuclear receptors.
- (C) DNA-binding domain (DBD): Highly conserved domain containing two zinc fingers that binds to specific sequences of DNA called hormone response elements (HRE).
- (D) Hinge region: Thought to be a flexible domain that connects the DBD with the LBD. Influences intracellular trafficking and subcellular distribution.
- (E) Ligand binding domain (LBD): Moderately conserved in sequence and highly conserved in structure between the various nuclear receptors. The structure of the LBD is referred to as an alpha helical sandwich fold in which three anti parallel alpha helices (the "sandwich filling") are flanked by two alpha helices on one side and three on the other (the "bread"). The ligand binding cavity is within the interior of the LBD and just below three anti parallel alpha helical sandwich "filling". Along with the DBD, the LBD contributes to the dimerization interface of the receptor and in addition, binds coactivator and corepressor proteins. The LBD also contains the activation function 2 (AF-2) whose action is dependent on the presence of bound ligand.
- (F) C-terminal domain: Highly variable in sequence between various nuclear receptors.
The N-terminal (A/B), DNA-binding (C), and ligand binding (E) domains are independently well folded and structurally stable while the hinge region (D) and optional C-terminal (F) domains may be conformationally flexible and disordered. Domains relative orientations are very different by comparing three known multi-domian crystal structures, two of them binding on DR1, one binding on DR4.
Mechanism of action
Nuclear receptors are multifunctional proteins that transduce signals of their cognate ligands. Nuclear receptors (NRs) may be classified into two broad classes according to their mechanism of action and subcellular distribution in the absence of ligand.
Small lipophilic substances such as natural hormones diffuse through the cell membrane and bind to nuclear receptors located in the cytosol (type I NR) or nucleus (type II NR) of the cell. Binding causes a conformational change in the receptor which, depending on the class of receptor, triggers a cascade of downstream events that direct the NRs to DNA transcription regulation sites which result in up or down-regulation of gene expression. In addition, two additional classes, type III which are a variant of type I, and type IV that bind DNA as monomers have also been identified.
Ligand binding to type I nuclear receptors in the cytosol results in the dissociation of heat shock proteins, homo-dimerization, translocation (i.e., active transport) from the cytoplasm into the cell nucleus, and binding to specific sequences of DNA known as hormone response elements (HREs). Type I nuclear receptors bind to HREs consisting of two half-sites separated by a variable length of DNA, and the second half-site has a sequence inverted from the first (inverted repeat). Type I nuclear receptors include members of subfamily 3, such as the androgen receptor, estrogen receptors, glucocorticoid receptor, and progesterone receptor.
It has been noted that some of the NR subfamily 2 nuclear receptors may bind to direct repeat instead of inverted repeat HREs. In addition, some nuclear receptors that bind either as monomers or dimers, with only a single DNA binding domain of the receptor attaching to a single half site HRE. These nuclear receptors are considered orphan receptors, as their endogenous ligands are still unknown.
Type II receptors, in contrast to type I, are retained in the nucleus regardless of the ligand binding status and in addition bind as hetero-dimers (usually with RXR) to DNA. In the absence of ligand, type II nuclear receptors are often complexed with corepressor proteins. Ligand binding to the nuclear receptor causes dissociation of corepressor and recruitment of coactivator proteins. Additional proteins including RNA polymerase are then recruited to the NR/DNA complex that transcribe DNA into messenger RNA.
Type III nuclear receptors (principally NR subfamily 2) are similar to type I receptors in that both classes bind to DNA as homodimers. However, type III nuclear receptors, in contrast to type I, bind to direct repeat instead of inverted repeat HREs.
Type IV nuclear receptors bind either as monomers or dimers, but only a single DNA binding domain of the receptor binds to a single half site HRE. Examples of type IV receptors are found in most of the NR subfamilies.
Nuclear receptors bound to hormone response elements recruit a significant number of other proteins (referred to as transcription coregulators) that facilitate or inhibit the transcription of the associated target gene into mRNA. The function of these coregulators are varied and include chromatin remodeling (making the target gene either more or less accessible to transcription) or a bridging function to stabilize the binding of other coregulatory proteins. Nuclear receptors may bind specifically to a number of coregulator proteins, and thereby influence cellular mechanisms of signal transduction both directly, as well as indirectly.
Binding of agonist ligands (see section below) to nuclear receptors induces a conformation of the receptor that preferentially binds coactivator proteins. These proteins often have an intrinsic histone acetyltransferase (HAT) activity, which weakens the association of histones to DNA, and therefore promotes gene transcription.
Binding of antagonist ligands to nuclear receptors in contrast induces a conformation of the receptor that preferentially binds corepressor proteins. These proteins, in turn, recruit histone deacetylases (HDACs), which strengthens the association of histones to DNA, and therefore represses gene transcription.
Agonism vs antagonism
Depending on the receptor involved, the chemical structure of the ligand and the tissue that is being affected, nuclear receptor ligands may display dramatically diverse effects ranging in a spectrum from agonism to antagonism to inverse agonism.
The activity of endogenous ligands (such as the hormones estradiol and testosterone) when bound to their cognate nuclear receptors is normally to upregulate gene expression. This stimulation of gene expression by the ligand is referred to as an agonist response. The agonistic effects of endogenous hormones can also be mimicked by certain synthetic ligands, for example, the glucocorticoid receptor anti-inflammatory drug dexamethasone. Agonist ligands work by inducing a conformation of the receptor which favors coactivator binding (see upper half of the figure to the right).
Other synthetic nuclear receptor ligands have no apparent effect on gene transcription in the absence of endogenous ligand. However they block the effect of agonist through competitive binding to the same binding site in the nuclear receptor. These ligands are referred to as antagonists. An example of antagonistic nuclear receptor drug is mifepristone which binds to the glucocorticoid and progesterone receptors and therefore blocks the activity of the endogenous hormones cortisol and progesterone respectively. Antagonist ligands work by inducing a conformation of the receptor which prevents coactivator and promotes corepressor binding (see lower half of the figure to the right).
Finally, some nuclear receptors promote a low level of gene transcription in the absence of agonists (also referred to as basal or constitutive activity). Synthetic ligands which reduce this basal level of activity in nuclear receptors are known as inverse agonists.
Selective receptor modulators
A number of drugs that work through nuclear receptors display an agonist response in some tissues and an antagonistic response in other tissues. This behavior may have substantial benefits since it may allow retaining the desired beneficial therapeutic effects of a drug while minimizing undesirable side effects. Drugs with this mixed agonist/antagonist profile of action are referred to as selective receptor modulators (SRMs). Examples include Selective Androgen Receptor Modulators (SARMs), Selective Estrogen Receptor Modulators (SERMs) and Selective Progesterone Receptor Modulators (SPRMs). The mechanism of action of SRMs may vary depending on the chemical structure of the ligand and the receptor involved, however it is thought that many SRMs work by promoting a conformation of the receptor that is closely balanced between agonism and antagonism. In tissues where the concentration of coactivator proteins is higher than corepressors, the equilibrium is shifted in the agonist direction. Conversely in tissues where corepressors dominate, the ligand behaves as an antagonist.
The most common mechanism of nuclear receptor action involves direct binding of the nuclear receptor to a DNA hormone response element. This mechanism is referred to as transactivation. However some nuclear receptors not only have the ability to directly bind to DNA, but also to other transcription factors. This binding often results in deactivation of the second transcription factor in a process known as transrepression. One example of a nuclear receptor that are able to transrepress is the glucocorticoid receptor (GR). Furthermore certain GR ligands known as Selective Glucocorticoid Receptor Agonists (SEGRAs) are able to activate GR in such a way that GR more strongly transrepresses than transactivates. This selectivity increases the separation between the desired antiinflammatory effects and undesired metabolic side effects of these selective glucocorticoids.
The classical direct effects of nuclear receptors on gene regulation normally takes hours before a functional effect is seen in cells because of the large number of intermediate steps between nuclear receptor activation and changes in protein expression levels. However it has been observed that some effects from the application of hormones such as estrogen occur within minutes which is inconsistent with the classical mechanism of nuclear receptor action. While the molecular target for these non-genomic effects of nuclear receptors has not been conclusively demonstrated, it has been hypothesized that there are variants of nuclear receptors which are membrane associated instead of being localized in the cytosol or nucleus. Furthermore these membrane associated receptors function through alternative signal transduction mechanisms not involving gene regulation.
|1||Thyroid Hormone Receptor-like||A||Thyroid hormone receptor||NR1A1||TRÎ±||Thyroid hormone receptor-Î±||THRA||thyroid hormone|
|NR1A2||TRÎ²||Thyroid hormone receptor-Î²||THRB|
|B||Retinoic acid receptor||NR1B1||RARÎ±||Retinoic acid receptor-Î±||RARA||vitamin A and related compounds|
|NR1B2||RARÎ²||Retinoic acid receptor-Î²||RARB|
|NR1B3||RARÎ³||Retinoic acid receptor-Î³||RARG|
|C||Peroxisome proliferator-activated receptor||NR1C1||PPARÎ±||Peroxisome proliferator-activated receptor-Î±||PPARA||fatty acids, prostaglandins|
|NR1C2||PPAR-Î²/Î´||Peroxisome proliferator-activated receptor-Î²/Î´||PPARD|
|NR1C3||PPARÎ³||Peroxisome proliferator-activated receptor-Î³||PPARG|
|F||RAR-related orphan receptor||NR1F1||RORÎ±||RAR-related orphan receptor-Î±||RORA||cholesterol, ATRA|
|NR1F2||RORÎ²||RAR-related orphan receptor-Î²||RORB|
|NR1F3||RORÎ³||RAR-related orphan receptor-Î³||RORC|
|H||Liver X receptor-like||NR1H3||LXRÎ±||Liver X receptor-Î±||NR1H3||oxysterols|
|NR1H2||LXRÎ²||Liver X receptor-Î²||NR1H2|
|NR1H4||FXR||Farnesoid X receptor||NR1H4|
|NR1H5||FXR-Î²||Farnesoid X receptor-Î²||NR1H5P|
|I||Vitamin D receptor-like||NR1I1||VDR||Vitamin D receptor||VDR||vitamin D|
|NR1I2||PXR||Pregnane X receptor||NR1I2||xenobiotics|
|NR1I3||CAR||Constitutive androstane receptor||NR1I3||androstane|
|X||NRs with two DNA binding domains||NR1X1||2DBD-NRÎ±|
|2||Retinoid X Receptor-like||A||Hepatocyte nuclear factor-4||NR2A1||HNF4Î±||Hepatocyte nuclear factor-4-Î±||HNF4A||fatty acids|
|NR2A2||HNF4Î³||Hepatocyte nuclear factor-4-Î³||HNF4G|
|B||Retinoid X receptor||NR2B1||RXRÎ±||Retinoid X receptor-Î±||RXRA||retinoids|
|NR2B2||RXRÎ²||Retinoid X receptor-Î²||RXRB|
|NR2B3||RXRÎ³||Retinoid X receptor-Î³||RXRG|
|C||Testicular receptor||NR2C1||TR2||Testicular receptor 2||NR2C1|
|NR2C2||TR4||Testicular receptor 4||NR2C2|
|E||TLX/PNR||NR2E1||TLX||Homologue of the Drosophila tailless gene||NR2E1|
|NR2E3||PNR||Photoreceptor cell-specific nuclear receptor||NR2E3|
|F||COUP/EAR||NR2F1||COUP-TFI||Chicken ovalbumin upstream promoter-transcription factor I||NR2F1|
|NR2F2||COUP-TFII||Chicken ovalbumin upstream promoter-transcription factor II||NR2F2|
|3||Estrogen Receptor-like||A||Estrogen receptor||NR3A1||ERÎ±||Estrogen receptor-Î±||ESR1||estrogens|
|B||Estrogen related receptor||NR3B1||ERRÎ±||Estrogen-related receptor-Î±||ESRRA|
|C||3-Ketosteroid receptors||NR3C1||GR||Glucocorticoid receptor||NR3C1||cortisol|
|4||Nerve Growth Factor IB-like||A||NGFIB/NURR1/NOR1||NR4A1||NGFIB||Nerve Growth factor IB||NR4A1|
|NR4A2||NURR1||Nuclear receptor related 1||NR4A2|
|NR4A3||NOR1||Neuron-derived orphan receptor 1||NR4A3|
|5||Steroidogenic Factor-like||A||SF1/LRH1||NR5A1||SF1||Steroidogenic factor 1||NR5A1||phosphatidylinositols|
|NR5A2||LRH-1||Liver receptor homolog-1||NR5A2||phosphatidylinositols|
|6||Germ Cell Nuclear Factor-like||A||GCNF||NR6A1||GCNF||Germ cell nuclear factor||NR6A1|
|0||Miscellaneous||B||DAX/SHP||NR0B1||DAX1||Dosage-sensitive sex reversal, adrenal hypoplasia critical region, on chromosome X, gene 1||NR0B1|
|NR0B2||SHP||Small heterodimer partner||NR0B2|
Below is a brief selection of key events in the history of nuclear receptor research.
- 1905 â€“ Ernest Starling coined the word hormone
- 1926 â€“ Edward Calvin Kendall and Tadeus Reichstein isolated and determined the structures of cortisone and thyroxine
- 1929 â€“ Adolf Butenandt and Edward Adelbert Doisy â€“ independently isolated and determined the structure of estrogen
- 1958 â€“ Elwood Jensen â€“ isolated the estrogen receptor
- 1980s â€“ cloning of the estrogen, glucocorticoid, and thyroid hormone receptors by Pierre Chambon, Ronald Evans, and BjÃ¶rn VennstrÃ¶m respectively
- 2004 â€“ Pierre Chambon, Ronald Evans, and Elwood Jensen were awarded the Albert Lasker Award for Basic Medical Research, an award that frequently precedes a Nobel Prize in Medicine
- PDB 3E00; Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP et al. (October 2008). "Structure of the intact PPAR-gamma-RXR-alpha nuclear receptor complex on DNA". Nature 456 (7220): 350â€“356. doi:10.1038/nature07413. PMC 2743566. PMID 19043829.
- Evans RM (1988). "The steroid and thyroid hormone receptor superfamily". Science 240 (4854): 889â€“95. doi:10.1126/science.3283939. PMID 3283939.
- Olefsky JM (2001). "Nuclear receptor minireview series". J. Biol. Chem. 276 (40): 36863â€“4. doi:10.1074/jbc.R100047200. PMID 11459855.
- Mangelsdorf DJ, Thummel C, Beato M, Herrlich P, Schutz G, Umesono K et al. (1995). "The nuclear receptor superfamily: the second decade". Cell 83 (6): 835â€“9. doi:10.1016/0092-8674(95)90199-X. PMID 8521507.
- Novac N, Heinzel T (2004). "Nuclear receptors: overview and classification". Curr Drug Targets Inflamm Allergy 3 (4): 335â€“46. doi:10.2174/1568010042634541. PMID 15584884.
- Nuclear Receptors Nomenclature C (1999). "A unified nomenclature system for the nuclear receptor superfamily". Cell 97 (2): 161â€“3. doi:10.1016/S0092-8674(00)80726-6. PMID 10219237.
- Laudet V (1997). "Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor". J. Mol. Endocrinol. 19 (3): 207â€“26. doi:10.1677/jme.0.0190207. PMID 9460643.
- Escriva H, Langlois MC, MendonÃ§a RL, Pierce R, Laudet V (May 1998). "Evolution and diversification of the nuclear receptor superfamily". Annals of the New York Academy of Sciences 839: 143â€“6. doi:10.1111/j.1749-6632.1998.tb10747.x. PMID 9629140.
- Reitzel AM, Pang K, Ryan JF, Mullikin JC, Martindale MQ, Baxevanis AD et al. (2011). "Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily?". Evodevo 2 (1): 3. doi:10.1186/2041-9139-2-3. PMC 3038971. PMID 21291545.
- Bridgham JT, Eick GN, Larroux C, Deshpande K, Harms MJ, Gauthier ME et al. (2010). "Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor". PLoS Biol. 8 (10): e1000497. doi:10.1371/journal.pbio.1000497. PMC 2950128. PMID 20957188.
- Sluder AE, Maina CV (April 2001). "Nuclear receptors in nematodes: themes and variations". Trends in Genetics : TIG 17 (4): 206â€“13. doi:10.1016/S0168-9525(01)02242-9. PMID 11275326.
- Zhang Z, Burch PE, Cooney AJ, Lanz RB, Pereira FA, Wu J et al. (2004). "Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome". Genome Res 14 (4): 580â€“90. doi:10.1101/gr.2160004. PMC 383302. PMID 15059999.
- Overington JP, Al-Lazikani B, Hopkins AL (2006). "How many drug targets are there?". Nature reviews. Drug discovery 5 (12): 993â€“6. doi:10.1038/nrd2199. PMID 17139284.
- Benoit G, Cooney A, Giguere V, Ingraham H, Lazar M, Muscat G et al. (2006). "International Union of Pharmacology. LXVI. Orphan nuclear receptors". Pharmacol. Rev. 58 (4): 798â€“836. doi:10.1124/pr.58.4.10. PMID 17132856.
- Mohan R, Heyman RA (2003). "Orphan nuclear receptor modulators". Curr Top Med Chem 3 (14): 1637â€“47. doi:10.2174/1568026033451709. PMID 14683519.
- Kumar R, Thompson EB (1999). "The structure of the nuclear hormone receptors". Steroids 64 (5): 310â€“9. doi:10.1016/S0039-128X(99)00014-8. PMID 10406480.
- Klinge CM (2000). "Estrogen receptor interaction with co-activators and co-repressors". Steroids 65 (5): 227â€“51. doi:10.1016/S0039-128X(99)00107-5. PMID 10751636.
- WÃ¤rnmark A, Treuter E, Wright AP, Gustafsson JÃ… (2003). "Activation functions 1 and 2 of nuclear receptors: molecular strategies for transcriptional activation". Mol. Endocrinol. 17 (10): 1901â€“9. doi:10.1210/me.2002-0384. PMID 12893880.
- Weatherman RV, Fletterick RJ, Scanlan TS (1999). "Nuclear-receptor ligands and ligand-binding domains". Annu. Rev. Biochem. 68: 559â€“81. doi:10.1146/annurev.biochem.68.1.559. PMID 10872460.
- Chandra V, Huang P, Potluri N, Wu D, Kim Y, Rastinejad F (March 2013). "Multidomain integration in the structure of the HNF-4Î± nuclear receptor complex". Nature 495 (7441): 394â€“398. doi:10.1038/nature11966. PMID 23485969.
- Lou X, Toresson G, Benod C, Suh JH, Philips KJ, Webb P, Gustafsson JA (February 2014). "Structure of the retinoid X receptor Î±-liver X receptor Î² (RXRÎ±-LXRÎ²) heterodimer on DNA". Nat. Struct. Mol. Biol. 21 (3): 277â€“281. doi:10.1038/nsmb.2778. PMID 24561505.
- PDB 2C7A; Roemer SC, Donham DC, Sherman L, Pon VH, Edwards DP, Churchill ME (December 2006). "Structure of the progesterone receptor-deoxyribonucleic acid complex: novel interactions required for binding to half-site response elements". Mol. Endocrinol. 20 (12): 3042â€“52. doi:10.1210/me.2005-0511. PMC 2532839. PMID 16931575.
- PDB 3L0L; Jin L, Martynowski D, Zheng S, Wada T, Xie W, Li Y (May 2010). "Structural basis for hydroxycholesterols as natural ligands of orphan nuclear receptor RORgamma". Mol. Endocrinol. 24 (5): 923â€“9. doi:10.1210/me.2009-0507. PMC 2870936. PMID 20203100.
- Linja MJ, Porkka KP, Kang Z, Savinainen KJ, JÃ¤nne OA, Tammela TL et al. (February 2004). "Expression of androgen receptor coregulators in prostate cancer". Clin. Cancer Res. 10 (3): 1032â€“40. doi:10.1158/1078-0432.CCR-0990-3. PMID 14871982.
- Klinge CM, Bodenner DL, Desai D, Niles RM, Traish AM (May 1997). "Binding of type II nuclear receptors and estrogen receptor to full and half-site estrogen response elements in vitro". Nucleic Acids Res. 25 (10): 1903â€“12. doi:10.1093/nar/25.10.1903. PMC 146682. PMID 9115356.
- Glass CK, Rosenfeld MG (2000). "The coregulator exchange in transcriptional functions of nuclear receptors". Genes Dev 14 (2): 121â€“41. doi:10.1101/gad.14.2.121. PMID 10652267.
- Aranda A, Pascual A (2001). "Nuclear hormone receptors and gene expression" (ABSTRACT). Physiol. Rev. 81 (3): 1269â€“304. PMID 11427696.
- Copland JA, Sheffield-Moore M, Koldzic-Zivanovic N, Gentry S, Lamprou G, Tzortzatou-Stathopoulou F, Zoumpourlis V, Urban RJ, Vlahopoulos SA (June 2009). "Sex steroid receptors in skeletal differentiation and epithelial neoplasia: is tissue-specific intervention possible?". BioEssays 31 (6): 629â€“41. doi:10.1002/bies.200800138. PMID 19382224.
- Brzozowski AM, Pike AC, Dauter Z, Hubbard RE, Bonn T, EngstrÃ¶m O et al. (1997). "Molecular basis of agonism and antagonism in the oestrogen receptor". Nature 389 (6652): 753â€“8. doi:10.1038/39645. PMID 9338790.
- Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA et al. (1998). "The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen". Cell 95 (7): 927â€“37. doi:10.1016/S0092-8674(00)81717-1. PMID 9875847.
- Gronemeyer H, Gustafsson JA, Laudet V (2004). "Principles for modulation of the nuclear receptor superfamily". Nature reviews. Drug discovery 3 (11): 950â€“64. doi:10.1038/nrd1551. PMID 15520817.
- Busch BB, Stevens WC J, Martin R, Ordentlich P, Zhou S, Sapp DW et al. (2004). "Identification of a selective inverse agonist for the orphan nuclear receptor estrogen-related receptor alpha". J. Med. Chem. 47 (23): 5593â€“6. doi:10.1021/jm049334f. PMID 15509154.
- Smith CL, O'Malley BW (2004). "Coregulator function: a key to understanding tissue specificity of selective receptor modulators". Endocr Rev 25 (1): 45â€“71. doi:10.1210/er.2003-0023. PMID 14769827.
- Pascual G, Glass CK (2006). "Nuclear receptors versus inflammation: mechanisms of transrepression". Trends Endocrinol Metab 17 (8): 321â€“7. doi:10.1016/j.tem.2006.08.005. PMID 16942889.
- BjÃ¶rnstrÃ¶m L, SjÃ¶berg M (2004). "Estrogen receptor-dependent activation of AP-1 via non-genomic signalling". Nucl Recept 2 (1): 3. doi:10.1186/1478-1336-2-3. PMC 434532. PMID 15196329.
- Zivadinovic D, Gametchu B, Watson CS (2005). "Membrane estrogen receptor-alpha levels in MCF-7 breast cancer cells predict cAMP and proliferation responses". Breast Cancer Res. 7 (1): R101â€“12. doi:10.1186/bcr958. PMC 1064104. PMID 15642158.
- Otte K, Kranz H, Kober I, Thompson P, Hoefer M, Haubold B, Remmel B, Voss H, Kaiser C, Albers M, Cheruvallath Z, Jackson D, Casari G, Koegl M, PÃ¤Ã¤bo S, Mous J, Kremoser C, Deuschle U (2003). "Identification of farnesoid X receptor beta as a novel mammalian nuclear receptor sensing lanosterol". Mol. Cell. Biol. 23 (3): 864â€“72. doi:10.1128/mcb.23.3.864-872.2003. PMC 140718. PMID 12529392.
- Wu W, Niles EG, El-Sayed N, Berriman M, LoVerde PT (2006). "Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: sixteen new members and a novel subfamily". Gene 366 (2): 303â€“15. doi:10.1016/j.gene.2005.09.013. PMID 16406405.
- Wu W, Niles EG, Hirai H, LoVerde PT (2007). "Evolution of a novel subfamily of nuclear receptors with members that each contain two DNA binding domains". BMC Evol Biol 7: 27. doi:10.1186/1471-2148-7-27. PMC 1810520. PMID 17319953.
- Tata JR (2005). "One hundred years of hormones". EMBO Rep. 6 (6): 490â€“6. doi:10.1038/sj.embor.7400444. PMC 1369102. PMID 15940278.
- Eukaryotic Linear Motif resource motif class LIG_CORNRBOX
- Eukaryotic Linear Motif resource motif class LIG_NRBOX
- Nuclear Receptors at the US National Library of Medicine Medical Subject Headings (MeSH)
- Vincent Laudet (2006). "The IUPHAR Compendium of the Pharmacology and Classification of the Nuclear Receptor Superfamily 2006E". Nuclear Receptor Compendium. The International Union of Basic and Clinical Pharmacology. Retrieved 2008-02-21.
- "Nuclear Receptor online journal". Home page. published by BioMed Central (no longer accepting submissions since May 2007). Retrieved 2008-02-21.
- "Nuclear Receptor Resource". Georgetown University. Retrieved 2008-02-21.
- "Nuclear Receptor Signaling Atlas (Receptors, Coactivators, Corepressors and Ligands)". The NURSA Consortium. Retrieved 2008-02-21.
an NIH-funded research consortium and database; includes open-access PubMed-indexed journal, Nuclear Receptor Signaling
- "Nuclear Receptor Resource". Jack Vanden Heuvel. Retrieved 2009-09-21.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Zinc finger, C4 type (two domains) Provide feedback
In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001628
Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [PUBMED:15242341, PUBMED:15242339]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators [PUBMED:15242339].
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [PUBMED:10529348, PUBMED:15963892, PUBMED:15718139, PUBMED:17210253, PUBMED:12665246]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [PUBMED:11179890]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
This entry represents the two C4-type zinc finger modules involved in DNA-binding.
More information about these proteins can be found at Protein of the Month: Zinc Fingers [PUBMED:].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||nucleus (GO:0005634)|
|Molecular function||sequence-specific DNA binding (GO:0043565)|
|zinc ion binding (GO:0008270)|
|sequence-specific DNA binding transcription factor activity (GO:0003700)|
|Biological process||regulation of transcription, DNA-templated (GO:0006355)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Number in seed:||26|
|Number in full:||9896|
|Average length of the domain:||66.60 aa|
|Average identity of full alignment:||47 %|
|Average coverage of the sequence by the domain:||14.68 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the zf-C4 domain has been found. There are 120 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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