spacer
spacer
Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Transcription/DNA PDB id
1hcq
Jmol
Contents
Protein chains
74 a.a. *
DNA/RNA
Metals
_ZN ×8
Waters ×158
* Residue conservation analysis
PDB id:
1hcq
Name: Transcription/DNA
Title: The crystal structure of the estrogen receptor DNA-binding domain bound to dna: how receptors discriminate between their response elements
Structure: DNA (5'- d( Cp Cp Ap Gp Gp Tp Cp Ap Cp Ap Gp Tp Gp Ap Cp Cp T p G)- 3'). Chain: c, g. Engineered: yes. DNA (5'- d( Cp Cp Ap Gp Gp Tp Cp Ap Cp Tp Gp Tp Gp Ap Cp Cp T p G)- 3'). Chain: d, h.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.204    
Authors: J.W.R.Schwabe,L.Chapman,J.T.Finch,D.Rhodes
Key ref: J.W.Schwabe et al. (1993). The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell, 75, 567-578. PubMed id: 8221895 DOI: 10.1016/0092-8674(93)90390-C
Date:
04-Jan-95     Release date:   23-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03372  (ESR1_HUMAN) -  Estrogen receptor
Seq:
Struc: 		 
Seq:
Struc: 		595 a.a.
74 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     5 terms  

 

 
DOI no: 10.1016/0092-8674(93)90390-C Cell 75:567-578 (1993)
PubMed id: 8221895  
 
 
The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements.
J.W.Schwabe, L.Chapman, J.T.Finch, D.Rhodes.
 
  ABSTRACT  
 
The nuclear hormone receptors are a superfamily of ligand-activated DNA-binding transcription factors. We have determined the crystal structure (at 2.4 A) of the fully specific complex between the DNA-binding domain from the estrogen receptor and DNA. The protein binds as a symmetrical dimer to its palindromic binding site consisting of two 6 bp consensus half sites with three intervening base pairs. This structure reveals how the protein recognizes its own half site sequence rather than that of the related glucocorticoid receptor, which differs by only two base pairs. Since all nuclear hormone receptors recognize one or the other of these two consensus half site sequences, this recognition mechanism applies generally to the whole receptor family.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21253649 S.M.Quintal, Q.A.dePaula, and N.P.Farrell (2011).
Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences.
  Metallomics, 3, 121-139.  
20047966 C.E.Mason, F.J.Shu, C.Wang, R.M.Session, R.G.Kallen, N.Sidell, T.Yu, M.H.Liu, E.Cheung, and C.B.Kallen (2010).
Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.
  Nucleic Acids Res, 38, 2355-2368.  
20197399 D.J.Schultz, N.S.Wickramasinghe, M.M.Ivanova, S.M.Isaacs, S.M.Dougherty, Y.Imbert-Fernandez, A.R.Cunningham, C.Chen, and C.M.Klinge (2010).
Anacardic acid inhibits estrogen receptor alpha-DNA binding and reduces target gene transcription and breast cancer cell proliferation.
  Mol Cancer Ther, 9, 594-605.  
20547749 J.D.Stender, K.Kim, T.H.Charn, B.Komm, K.C.Chang, W.L.Kraus, C.Benner, C.K.Glass, and B.S.Katzenellenbogen (2010).
Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation.
  Mol Cell Biol, 30, 3943-3955.  
19946606 S.L.Nott, Y.Huang, A.Kalkanoglu, K.Harper, M.Chen, S.F.Paoni, B.M.Fenton, and M.Muyan (2010).
Designer monotransregulators provide a basis for a transcriptional therapy for de novo endocrine-resistant breast cancer.
  Mol Med, 16, 10-18.  
  20087432 I.J.McEwan, and A.M.Nardulli (2009).
Nuclear hormone receptor architecture - form and dynamics: The 2009 FASEB Summer Conference on Dynamic Structure of the Nuclear Hormone Receptors.
  Nucl Recept Signal, 7, e011.  
19666041 R.Kumar, and G.Litwack (2009).
Structural and functional relationships of the steroid hormone receptors' N-terminal transactivation domain.
  Steroids, 74, 877-883.  
19321454 S.L.Nott, Y.Huang, X.Li, B.R.Fluharty, X.Qiu, W.V.Welshons, S.Yeh, and M.Muyan (2009).
Genomic Responses from the Estrogen-responsive Element-dependent Signaling Pathway Mediated by Estrogen Receptor {alpha} Are Required to Elicit Cellular Alterations.
  J Biol Chem, 284, 15277-15288.  
19447913 V.J.McAlister, and G.E.Christie (2009).
Analysis of DNA binding by a eubacterial zinc finger transcription factor.
  J Bacteriol, 191, 4513-4521.  
19796154 Y.Nakagawa, and V.C.Henrich (2009).
Arthropod nuclear receptors and their role in molting.
  FEBS J, 276, 6128-6157.  
18651760 M.D.Krasowski, E.J.Reschly, and S.Ekins (2008).
Intrinsic disorder in nuclear hormone receptors.
  J Proteome Res, 7, 4359-4372.  
18179891 R.W.Collin, E.Kalay, M.Tariq, T.Peters, B.van der Zwaag, H.Venselaar, J.Oostrik, K.Lee, Z.M.Ahmed, R.Caylan, Y.Li, H.A.Spierenburg, E.Eyupoglu, A.Heister, S.Riazuddin, E.Bahat, M.Ansar, S.Arslan, B.Wollnik, H.G.Brunner, C.W.Cremers, A.Karaguzel, W.Ahmad, F.P.Cremers, G.Vriend, T.B.Friedman, S.Riazuddin, S.M.Leal, and H.Kremer (2008).
Mutations of ESRRB encoding estrogen-related receptor beta cause autosomal-recessive nonsyndromic hearing impairment DFNB35.
  Am J Hum Genet, 82, 125-138.  
  19337586 S.L.Nott, Y.Huang, B.R.Fluharty, A.M.Sokolov, M.Huang, C.Cox, and M.Muyan (2008).
Do Estrogen Receptor beta Polymorphisms Play A Role in the Pharmacogenetics of Estrogen Signaling?
  Curr Pharmacogenomics Person Med, 6, 239-259.  
18049881 T.Krusiński, M.Wietrzych, I.Grad, A.Ozyhar, and P.Dobryszycki (2008).
Equilibrium Analysis of the DNA Binding Domain of the Ultraspiracle Protein Interaction with the Response Element from the hsp27 Gene Promoter-the Application of Molecular Beacon Technology.
  J Fluoresc, 18, 1.  
17986456 V.Bourdeau, J.Deschênes, D.Laperrière, M.Aid, J.H.White, and S.Mader (2008).
Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells.
  Nucleic Acids Res, 36, 76-93.  
18403199 X.Li, J.Huang, B.R.Fluharty, Y.Huang, S.L.Nott, and M.Muyan (2008).
What are comparative studies telling us about the mechanism of ERbeta action in the ERE-dependent E2 signaling pathway?
  J Steroid Biochem Mol Biol, 109, 266-272.  
17269124 A.Marabotti, G.Colonna, and A.Facchiano (2007).
New computational strategy to analyze the interactions of ERalpha and ERbeta with different ERE sequences.
  J Comput Chem, 28, 1031-1041.  
17933688 C.Kremoser, M.Albers, T.P.Burris, U.Deuschle, and M.Koegl (2007).
Panning for SNuRMs: using cofactor profiling for the rational discovery of selective nuclear receptor modulators.
  Drug Discov Today, 12, 860-869.  
17478511 D.Nguyen, M.Bail, G.Pesant, V.N.Dupont, E.Rouault, J.Deschênes, W.Rocha, G.Melançon, S.V.Steinberg, and S.Mader (2007).
Rational design of an estrogen receptor mutant with altered DNA-binding specificity.
  Nucleic Acids Res, 35, 3465-3477.  
17521420 J.L.Jiménez, B.Hegemann, J.R.Hutchins, J.M.Peters, and R.Durbin (2007).
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.
  Genome Biol, 8, R90.  
17320364 M.M.McGrane (2007).
Vitamin A regulation of gene expression: molecular mechanism of a prototype gene.
  J Nutr Biochem, 18, 497-508.  
17600153 M.R.Calgaro, M.d.e. .O.Neto, A.C.Figueira, M.A.Santos, R.V.Portugal, C.A.Guzzi, D.M.Saidemberg, L.Bleicher, J.Vernal, P.Fernandez, H.Terenzi, M.S.Palma, and I.Polikarpov (2007).
Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface.
  Protein Sci, 16, 1762-1772.  
17566103 N.G.Nickols, and P.B.Dervan (2007).
Suppression of androgen receptor-mediated gene expression by a sequence-specific DNA-binding polyamide.
  Proc Natl Acad Sci U S A, 104, 10418-10423.  
17426379 R.P.Metpally, R.Vigneshwar, and R.Sowdhamini (2007).
Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis.
  J Biosci, 32, 43-50.  
17157789 L.H.Wang, X.Y.Yang, X.Zhang, P.An, H.J.Kim, J.Huang, R.Clarke, C.K.Osborne, J.K.Inman, E.Appella, and W.L.Farrar (2006).
Disruption of estrogen receptor DNA-binding domain and related intramolecular communication restores tamoxifen sensitivity in resistant breast cancer.
  Cancer Cell, 10, 487-499.  
  16880568 M.D.Sam, M.A.Abbani, D.Cascio, R.C.Johnson, and R.T.Clubb (2006).
Crystallization, dehydration and preliminary X-ray analysis of excisionase (Xis) proteins cooperatively bound to DNA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 825-828.  
18369406 M.Marino, P.Galluzzo, and P.Ascenzi (2006).
Estrogen signaling multiple pathways to impact gene transcription.
  Curr Genomics, 7, 497-508.  
16683264 N.W.Allen, and N.L.Thompson (2006).
Ligand binding by estrogen receptor beta attached to nanospheres measured by fluorescence correlation spectroscopy.
  Cytometry A, 69, 524-532.  
16914190 P.Ascenzi, A.Bocedi, and M.Marino (2006).
Structure-function relationship of estrogen receptor alpha and beta: impact on human health.
  Mol Aspects Med, 27, 299-402.  
16931575 S.C.Roemer, D.C.Donham, L.Sherman, V.H.Pon, D.P.Edwards, and M.E.Churchill (2006).
Structure of the progesterone receptor-deoxyribonucleic acid complex: novel interactions required for binding to half-site response elements.
  Mol Endocrinol, 20, 3042-3052.
PDB code: 2c7a
15930325 A.L.Filby, and C.R.Tyler (2005).
Molecular characterization of estrogen receptors 1, 2a, and 2b and their tissue and ontogenic expression profiles in fathead minnow (Pimephales promelas).
  Biol Reprod, 73, 648-662.  
16135815 F.F.Zheng, R.C.Wu, C.L.Smith, and B.W.O'Malley (2005).
Rapid estrogen-induced phosphorylation of the SRC-3 coactivator occurs in an extranuclear complex containing estrogen receptor.
  Mol Cell Biol, 25, 8273-8284.  
16085755 J.E.Donald, and E.I.Shakhnovich (2005).
Predicting specificity-determining residues in two large eukaryotic transcription factor families.
  Nucleic Acids Res, 33, 4455-4465.  
15790569 S.Kamalakaran, S.K.Radhakrishnan, and W.T.Beck (2005).
Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.
  J Biol Chem, 280, 21491-21497.  
  16971966 Y.S.Zhu (2005).
Molecular Basis of Steroid Action in the Prostate.
  Cellscience, 1, 27-55.  
15142590 D.H.Wicaksono, T.Ebihara, H.Funabashi, M.Mie, Y.Yanagida, M.Aizawa, and E.Kobatake (2004).
On-chip biosensing of estrogen receptor-alpha at single molecular level.
  Biosens Bioelectron, 19, 1573-1579.  
15123600 G.Fiermonte, F.De Leonardis, S.Todisco, L.Palmieri, F.M.Lasorsa, and F.Palmieri (2004).
Identification of the mitochondrial ATP-Mg/Pi transporter. Bacterial expression, reconstitution, functional characterization, and tissue distribution.
  J Biol Chem, 279, 30722-30730.  
15450240 K.H.Pearce, M.A.Iannone, C.A.Simmons, and J.G.Gray (2004).
Discovery of novel nuclear receptor modulating ligands: an integral role for peptide interaction profiling.
  Drug Discov Today, 9, 741-751.  
14704356 M.C.Frith, U.Hansen, J.L.Spouge, and Z.Weng (2004).
Finding functional sequence elements by multiple local alignment.
  Nucleic Acids Res, 32, 189-200.  
15037741 P.L.Shaffer, A.Jivan, D.E.Dollins, F.Claessens, and D.T.Gewirth (2004).
Structural basis of androgen receptor binding to selective androgen response elements.
  Proc Natl Acad Sci U S A, 101, 4758-4763.
PDB code: 1r4i
14871313 Y.Umemura, T.Ishiduka, R.Yamamoto, and M.Esaka (2004).
The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain.
  Plant J, 37, 741-749.  
14612399 C.Patrone, T.N.Cassel, K.Pettersson, Y.S.Piao, G.Cheng, P.Ciana, A.Maggi, M.Warner, J.A.Gustafsson, and M.Nord (2003).
Regulation of postnatal lung development and homeostasis by estrogen receptor beta.
  Mol Cell Biol, 23, 8542-8552.  
  14644319 D.Anderson, T.E.Schmid, A.Baumgartner, E.Cemeli-Carratala, M.H.Brinkworth, and J.M.Wood (2003).
Oestrogenic compounds and oxidative stress (in human sperm and lymphocytes in the Comet assay).
  Mutat Res, 544, 173-178.  
12897800 H.Nakase, Y.Takahama, and Y.Akamatsu (2003).
Effect of CpG methylation on RAG1/RAG2 reactivity: implications of direct and indirect mechanisms for controlling V(D)J cleavage.
  EMBO Rep, 4, 774-780.  
14640689 J.C.Payne, B.W.Rous, A.L.Tenderholt, and H.A.Godwin (2003).
Spectroscopic determination of the binding affinity of zinc to the DNA-binding domains of nuclear hormone receptors.
  Biochemistry, 42, 14214-14224.  
14592980 S.Devarakonda, J.M.Harp, Y.Kim, A.Ozyhar, and F.Rastinejad (2003).
Structure of the heterodimeric ecdysone receptor DNA-binding complex.
  EMBO J, 22, 5827-5840.
PDB codes: 1r0n 1r0o
12527760 S.S.Krishna, I.Majumdar, and N.V.Grishin (2003).
Structural classification of zinc fingers: survey and summary.
  Nucleic Acids Res, 31, 532-550.  
11748221 A.Dintilhac, and J.Bernués (2002).
HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences.
  J Biol Chem, 277, 7021-7028.  
11818562 A.Koide, S.Abbatiello, L.Rothgery, and S.Koide (2002).
Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor.
  Proc Natl Acad Sci U S A, 99, 1253-1258.  
11877418 J.A.Tan, S.H.Hall, K.G.Hamil, G.Grossman, P.Petrusz, and F.S.French (2002).
Protein inhibitors of activated STAT resemble scaffold attachment factors and function as interacting nuclear receptor coregulators.
  J Biol Chem, 277, 16993-17001.  
12211013 J.Bredenberg, and L.Nilsson (2002).
Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.
  Proteins, 49, 24-36.  
12209130 J.R.Tata (2002).
Signalling through nuclear receptors.
  Nat Rev Mol Cell Biol, 3, 702-710.  
12411447 L.Björnström, and M.Sjöberg (2002).
Mutations in the estrogen receptor DNA-binding domain discriminate between the classical mechanism of action and cross-talk with Stat5b and activating protein 1 (AP-1).
  J Biol Chem, 277, 48479-48483.  
11980721 P.L.Shaffer, and D.T.Gewirth (2002).
Structural basis of VDR-DNA interactions on direct repeat response elements.
  EMBO J, 21, 2242-2252.
PDB codes: 1kb2 1kb4 1kb6
11948698 P.W.Jurutka, P.N.MacDonald, S.Nakajima, J.C.Hsieh, P.D.Thompson, G.K.Whitfield, M.A.Galligan, C.A.Haussler, and M.R.Haussler (2002).
Isolation of baculovirus-expressed human vitamin D receptor: DNA responsive element interactions and phosphorylation of the purified receptor.
  J Cell Biochem, 85, 435-457.  
11891761 R.Sanchez, D.Nguyen, W.Rocha, J.H.White, and S.Mader (2002).
Diversity in the mechanisms of gene regulation by estrogen receptors.
  Bioessays, 24, 244-254.  
12635173 S.Ali, and R.C.Coombes (2002).
Endocrine-responsive breast cancer and strategies for combating resistance.
  Nat Rev Cancer, 2, 101-112.  
12360281 T.J.Powles (2002).
Anti-oestrogenic prevention of breast cancer--the make or break point.
  Nat Rev Cancer, 2, 787-794.  
11452016 C.M.Klinge (2001).
Estrogen receptor interaction with estrogen response elements.
  Nucleic Acids Res, 29, 2905-2919.  
11554444 D.E.Wilcox, A.D.Schenk, B.M.Feldman, and Y.Xu (2001).
Oxidation of zinc-binding cysteine residues in transcription factor proteins.
  Antioxid Redox Signal, 3, 549-564.  
11297428 H.Matsuno, K.Niikura, and Y.Okahata (2001).
Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 mhz quartz crystal microbalance.
  Biochemistry, 40, 3615-3622.  
11432742 I.Grad, A.Niedziela-Majka, M.Kochman, and A.Ozyhar (2001).
Analysis of Usp DNA binding domain targeting reveals critical determinants of the ecdysone receptor complex interaction with the response element.
  Eur J Biochem, 268, 3751-3758.  
11181953 K.Pettersson, and J.A.Gustafsson (2001).
Role of estrogen receptor beta in estrogen action.
  Annu Rev Physiol, 63, 165-192.  
11380259 N.Greenfield, V.Vijayanathan, T.J.Thomas, M.A.Gallo, and T.Thomas (2001).
Increase in the stability and helical content of estrogen receptor alpha in the presence of the estrogen response element: analysis by circular dichroism spectroscopy.
  Biochemistry, 40, 6646-6652.  
11292843 N.V.Grishin (2001).
Treble clef finger--a functionally diverse zinc-binding structural motif.
  Nucleic Acids Res, 29, 1703-1714.  
11406412 S.Khorasanizadeh, and F.Rastinejad (2001).
Nuclear-receptor interactions on DNA-response elements.
  Trends Biochem Sci, 26, 384-390.  
11226231 V.Dolce, G.Fiermonte, M.J.Runswick, F.Palmieri, and J.E.Walker (2001).
The human mitochondrial deoxynucleotide carrier and its role in the toxicity of nucleoside antivirals.
  Proc Natl Acad Sci U S A, 98, 2284-2288.  
  10859169 A.Antebi, W.H.Yeh, D.Tait, E.M.Hedgecock, and D.L.Riddle (2000).
daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans.
  Genes Dev, 14, 1512-1527.  
10760049 D.B.Defranco (2000).
Role of molecular chaperones in subnuclear trafficking of glucocorticoid receptors.
  Kidney Int, 57, 1241-1249.  
10679372 D.J.Segal, and C.F.Barbas (2000).
Design of novel sequence-specific DNA-binding proteins.
  Curr Opin Chem Biol, 4, 34-39.  
10766868 E.Schoenmakers, G.Verrijdt, B.Peeters, G.Verhoeven, W.Rombauts, and F.Claessens (2000).
Differences in DNA binding characteristics of the androgen and glucocorticoid receptors can determine hormone-specific responses.
  J Biol Chem, 275, 12290-12297.  
10698945 F.Rastinejad, T.Wagner, Q.Zhao, and S.Khorasanizadeh (2000).
Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1.
  EMBO J, 19, 1045-1054.
PDB code: 1dsz
10619841 F.T.Tsai, and P.B.Sigler (2000).
Structural basis of preinitiation complex assembly on human pol II promoters.
  EMBO J, 19, 25-36.
PDB code: 1c9b
10617653 H.Poukka, P.Aarnisalo, H.Santti, O.A.Jänne, and J.J.Palvimo (2000).
Coregulator small nuclear RING finger protein (SNURF) enhances Sp1- and steroid receptor-mediated transcription by different mechanisms.
  J Biol Chem, 275, 571-579.  
10736185 I.Anderson, and J.Gorski (2000).
Estrogen receptor alpha interaction with estrogen response element half-sites from the rat prolactin gene.
  Biochemistry, 39, 3842-3847.  
  10898790 L.Zhu, J.Wilken, N.B.Phillips, U.Narendra, G.Chan, S.M.Stratton, S.B.Kent, and M.A.Weiss (2000).
Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers.
  Genes Dev, 14, 1750-1764.
PDB code: 1lpv
10871398 M.Boyer, N.Poujol, E.Margeat, and C.A.Royer (2000).
Quantitative characterization of the interaction between purified human estrogen receptor alpha and DNA using fluorescence anisotropy.
  Nucleic Acids Res, 28, 2494-2502.  
11250728 M.Ruff, M.Gangloff, J.M.Wurtz, and D.Moras (2000).
Estrogen receptor transcription and transactivation: Structure-function relationship in DNA- and ligand-binding domains of estrogen receptors.
  Breast Cancer Res, 2, 353-359.  
10801972 N.C.Horton, and J.J.Perona (2000).
Crystallographic snapshots along a protein-induced DNA-bending pathway.
  Proc Natl Acad Sci U S A, 97, 5729-5734.
PDB codes: 1eoo 1eop
  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.
  Genome Biol, 1, REVIEWS001.  
10913286 P.J.van Tilborg, M.Czisch, F.A.Mulder, G.E.Folkers, A.M.Bonvin, M.Nair, R.Boelens, and R.Kaptein (2000).
Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site.
  Biochemistry, 39, 8747-8757.  
10913246 R.M.Whittal, C.C.Benz, G.Scott, J.Semyonov, A.L.Burlingame, and M.A.Baldwin (2000).
Preferential oxidation of zinc finger 2 in estrogen receptor DNA-binding domain prevents dimerization and, hence, DNA binding.
  Biochemistry, 39, 8406-8417.  
10410794 C.Wolberger (1999).
Multiprotein-DNA complexes in transcriptional regulation.
  Annu Rev Biophys Biomol Struct, 28, 29-56.  
  9858592 H.Greschik, J.M.Wurtz, P.Hublitz, F.Köhler, D.Moras, and R.Schüle (1999).
Characterization of the DNA-binding and dimerization properties of the nuclear orphan receptor germ cell nuclear factor.
  Mol Cell Biol, 19, 690-703.  
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
  Proteins, 35, 114-131.  
10587460 J.C.Hsieh, G.K.Whitfield, A.K.Oza, H.T.Dang, J.N.Price, M.A.Galligan, P.W.Jurutka, P.D.Thompson, C.A.Haussler, and M.R.Haussler (1999).
Characterization of unique DNA-binding and transcriptional-activation functions in the carboxyl-terminal extension of the zinc finger region in the human vitamin D receptor.
  Biochemistry, 38, 16347-16358.  
10542063 J.P.Charles, T.Shinoda, and Y.Chinzei (1999).
Characterization and DNA-binding properties of GRF, a novel monomeric binding orphan receptor related to GCNF and betaFTZ-F1.
  Eur J Biochem, 266, 181-190.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10026278 P.J.van Tilborg, F.A.Mulder, M.M.de Backer, M.Nair, E.C.van Heerde, G.Folkers, P.T.van der Saag, Y.Karimi-Nejad, R.Boelens, and R.Kaptein (1999).
Millisecond to microsecond time scale dynamics of the retinoid X and retinoic acid receptor DNA-binding domains and dimeric complex formation.
  Biochemistry, 38, 1951-1956.  
10438541 S.Chusacultanachai, K.A.Glenn, A.O.Rodriguez, E.K.Read, J.F.Gardner, B.S.Katzenellenbogen, and D.J.Shapiro (1999).
Analysis of estrogen response element binding by genetically selected steroid receptor DNA binding domain mutants exhibiting altered specificity and enhanced affinity.
  J Biol Chem, 274, 23591-23598.  
10512803 S.Sen, and L.Nilsson (1999).
Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.
  Biophys J, 77, 1782-1800.  
9558340 C.Massaad, X.Coumoul, M.Sabbah, M.Garlatti, G.Redeuilh, and R.Barouki (1998).
Properties of overlapping EREs: synergistic activation of transcription and cooperative binding of ER.
  Biochemistry, 37, 6023-6032.  
9556570 C.Tzagarakis-Foster, and M.L.Privalsky (1998).
Phosphorylation of thyroid hormone receptors by protein kinase A regulates DNA recognition by specific inhibition of receptor monomer binding.
  J Biol Chem, 273, 10926-10932.  
  9821279 D.E.Mossakowska (1998).
Expression of nuclear hormone receptors in Escherichia coli.
  Curr Opin Biotechnol, 9, 502-505.  
9600906 D.M.Tanenbaum, Y.Wang, S.P.Williams, and P.B.Sigler (1998).
Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains.
  Proc Natl Acad Sci U S A, 95, 5998-6003.
PDB code: 1a52
9708984 H.Terenzi, P.M.Alzari, and M.M.Zakin (1998).
Structural features involved in the formation of a complex between the monomeric or the dimeric form of the rev-erb beta DNA-binding domain and its DNA reactive sites.
  Biochemistry, 37, 11488-11495.  
9597142 J.D.Klemm, S.L.Schreiber, and G.R.Crabtree (1998).
Dimerization as a regulatory mechanism in signal transduction.
  Annu Rev Immunol, 16, 569-592.  
  9528764 J.R.Wood, G.L.Greene, and A.M.Nardulli (1998).
Estrogen response elements function as allosteric modulators of estrogen receptor conformation.
  Mol Cell Biol, 18, 1927-1934.  
9792632 M.D.Driscoll, G.Sathya, M.Muyan, C.M.Klinge, R.Hilf, and R.A.Bambara (1998).
Sequence requirements for estrogen receptor binding to estrogen response elements.
  J Biol Chem, 273, 29321-29330.  
9580693 M.Vögtli, C.Elke, M.O.Imhof, and M.Lezzi (1998).
High level transactivation by the ecdysone receptor complex at the core recognition motif.
  Nucleic Acids Res, 26, 2407-2414.  
9660968 Q.Zhao, S.Khorasanizadeh, Y.Miyoshi, M.A.Lazar, and F.Rastinejad (1998).
Structural elements of an orphan nuclear receptor-DNA complex.
  Mol Cell, 1, 849-861.
PDB code: 1a6y
9665167 R.B.Turner, D.L.Smith, M.E.Zawrotny, M.F.Summers, M.C.Posewitz, and D.R.Winge (1998).
Solution structure of a zinc domain conserved in yeast copper-regulated transcription factors.
  Nat Struct Biol, 5, 551-555.
PDB code: 1co4
  9671457 V.Boonyaratanakornkit, V.Melvin, P.Prendergast, M.Altmann, L.Ronfani, M.E.Bianchi, L.Taraseviciene, S.K.Nordeen, E.A.Allegretto, and D.P.Edwards (1998).
High-mobility group chromatin proteins 1 and 2 functionally interact with steroid hormone receptors to enhance their DNA binding in vitro and transcriptional activity in mammalian cells.
  Mol Cell Biol, 18, 4471-4487.  
  9023209 A.L.Donner, P.A.Carlson, and G.B.Koudelka (1997).
Dimerization specificity of P22 and 434 repressors is determined by multiple polypeptide segments.
  J Bacteriol, 179, 1253-1261.  
9395481 C.M.Klinge, B.F.Silver, M.D.Driscoll, G.Sathya, R.A.Bambara, and R.Hilf (1997).
Chicken ovalbumin upstream promoter-transcription factor interacts with estrogen receptor, binds to estrogen response elements and half-sites, and inhibits estrogen-induced gene expression.
  J Biol Chem, 272, 31465-31474.  
9049312 D.Curtis, D.K.Treiber, F.Tao, P.D.Zamore, J.R.Williamson, and R.Lehmann (1997).
A CCHC metal-binding domain in Nanos is essential for translational regulation.
  EMBO J, 16, 834-843.  
9251777 D.Kosztin, T.C.Bishop, and K.Schulten (1997).
Binding of the estrogen receptor to DNA. The role of waters.
  Biophys J, 73, 557-570.  
9218433 D.S.Sem, D.R.Casimiro, S.A.Kliewer, J.Provencal, R.M.Evans, and P.E.Wright (1997).
NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear orphan receptor, human estrogen related receptor-2. The carboxyl-terminal extension to the zinc-finger region is unstructured in the free form of the protein.
  J Biol Chem, 272, 18038-18043.  
  9345851 G.Capranico, M.Binaschi, M.E.Borgnetto, F.Zunino, and M.Palumbo (1997).
A protein-mediated mechanism for the DNA sequence-specific action of topoisomerase II poisons.
  Trends Pharmacol Sci, 18, 323-329.  
9342356 G.E.Carney, A.A.Wade, R.Sapra, E.S.Goldstein, and M.Bender (1997).
DHR3, an ecdysone-inducible early-late gene encoding a Drosophila nuclear receptor, is required for embryogenesis.
  Proc Natl Acad Sci U S A, 94, 12024-12029.  
8995424 G.Jiang, and F.M.Sladek (1997).
The DNA binding domain of hepatocyte nuclear factor 4 mediates cooperative, specific binding to DNA and heterodimerization with the retinoid X receptor alpha.
  J Biol Chem, 272, 1218-1225.  
  9343418 G.Jiang, U.Lee, and F.M.Sladek (1997).
Proposed mechanism for the stabilization of nuclear receptor DNA binding via protein dimerization.
  Mol Cell Biol, 17, 6546-6554.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
9287161 H.Berglund, M.Wolf-Watz, T.Lundbäck, S.van den Berg, and T.Härd (1997).
Structure and dynamics of the glucocorticoid receptor DNA-binding domain: comparison of wild type and a mutant with altered specificity.
  Biochemistry, 36, 11188-11197.  
  9154816 J.Kim, G.de Haan, A.M.Nardulli, and D.J.Shapiro (1997).
Prebending the estrogen response element destabilizes binding of the estrogen receptor DNA binding domain.
  Mol Cell Biol, 17, 3173-3180.  
9032063 J.W.Schwabe (1997).
The role of water in protein-DNA interactions.
  Curr Opin Struct Biol, 7, 126-134.  
  9570132 K.Grandien, A.Berkenstam, and J.A.Gustafsson (1997).
The estrogen receptor gene: promoter organization and expression.
  Int J Biochem Cell Biol, 29, 1343-1369.  
9346945 M.A.Kuntz, and D.J.Shapiro (1997).
Dimerizing the estrogen receptor DNA binding domain enhances binding to estrogen response elements.
  J Biol Chem, 272, 27949-27956.  
9100018 M.K.Bhat, P.McPhie, and S.Cheng (1997).
Critical role of glutamine 252 in the hormone-dependent transcriptional activity of the thyroid hormone beta1 nuclear receptor.
  Biochemistry, 36, 4233-4239.  
9374531 M.S.Ozers, J.J.Hill, K.Ervin, J.R.Wood, A.M.Nardulli, C.A.Royer, and J.Gorski (1997).
Equilibrium binding of estrogen receptor with DNA using fluorescence anisotropy.
  J Biol Chem, 272, 30405-30411.  
9033395 P.Doesburg, C.W.Kuil, C.A.Berrevoets, K.Steketee, P.W.Faber, E.Mulder, A.O.Brinkmann, and J.Trapman (1997).
Functional in vivo interaction between the amino-terminal, transactivation domain and the ligand binding domain of the androgen receptor.
  Biochemistry, 36, 1052-1064.  
9325313 P.Pace, J.Taylor, S.Suntharalingam, R.C.Coombes, and S.Ali (1997).
Human estrogen receptor beta binds DNA in a manner similar to and dimerizes with estrogen receptor alpha.
  J Biol Chem, 272, 25832-25838.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9242648 S.M.Cowley, S.Hoare, S.Mosselman, and M.G.Parker (1997).
Estrogen receptors alpha and beta form heterodimers on DNA.
  J Biol Chem, 272, 19858-19862.  
9129808 T.C.Bishop, D.Kosztin, and K.Schulten (1997).
How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry.
  Biophys J, 72, 2056-2067.  
  9168467 Y.Tang, C.Ramakrishnan, J.Thomas, and D.B.DeFranco (1997).
A role for HDJ-2/HSDJ in correcting subnuclear trafficking, transactivation, and transrepression defects of a glucocorticoid receptor zinc finger mutant.
  Mol Biol Cell, 8, 795-809.  
  8622645 B.D.Lemon, and L.P.Freedman (1996).
Selective effects of ligands on vitamin D3 receptor- and retinoid X receptor-mediated gene activation in vivo.
  Mol Cell Biol, 16, 1006-1016.  
8702636 C.C.Nelson, S.C.Hendy, J.S.Faris, and P.J.Romaniuk (1996).
Retinoid X receptor alters the determination of DNA binding specificity by the P-box amino acids of the thyroid hormone receptor.
  J Biol Chem, 271, 19464-19474.  
  9000009 D.A.Erlanson, M.Chytil, and G.L.Verdine (1996).
The leucine zipper domain controls the orientation of AP-1 in the NFAT.AP-1.DNA complex.
  Chem Biol, 3, 981-991.  
8617792 D.Conte, S.Narindrasorasak, and B.Sarkar (1996).
In vivo and in vitro iron-replaced zinc finger generates free radicals and causes DNA damage.
  J Biol Chem, 271, 5125-5130.  
8761938 D.G.Mottershead, P.Polly, R.J.Lyons, R.L.Sutherland, and C.K.Watts (1996).
High activity, soluble, bacterially expressed human vitamin D receptor and its ligand binding domain.
  J Cell Biochem, 61, 325-337.  
8734007 J.H.Pinter, C.Deep, and O.K.Park-Sarge (1996).
Progesterone receptors: expression and regulation in the mammalian ovary.
  Clin Obstet Gynecol, 39, 424-435.  
8723335 J.W.Schwabe (1996).
Transcriptional control: how nuclear receptors get turned on.
  Curr Biol, 6, 372-374.  
  9004761 L.S.Yasui, A.Hughes, and E.R.DeSombre (1996).
DNA damage induction by 125I-estrogen.
  Acta Oncol, 35, 841-847.  
8994885 M.A.Navia (1996).
Protein-drug complexes important for immunoregulation and organ transplantation.
  Curr Opin Struct Biol, 6, 838-847.  
8651621 M.Beato, M.Truss, and S.Chávez (1996).
Control of transcription by steroid hormones.
  Ann N Y Acad Sci, 784, 93.  
  8947052 M.P.Kladde, M.Xu, and R.T.Simpson (1996).
Direct study of DNA-protein interactions in repressed and active chromatin in living cells.
  EMBO J, 15, 6290-6300.  
17029807 T.Härd, and T.Lundbäck (1996).
Thermodynamics of sequence-specific protein-DNA interactions.
  Biophys Chem, 62, 121-139.  
8643475 T.Lundbäck, and T.Härd (1996).
Sequence-specific DNA-binding dominated by dehydration.
  Proc Natl Acad Sci U S A, 93, 4754-4759.  
  7891721 A.H.Swirnoff, and J.Milbrandt (1995).
DNA-binding specificity of NGFI-A and related zinc finger transcription factors.
  Mol Cell Biol, 15, 2275-2287.  
7625690 A.Klug (1995).
Gene regulatory proteins and their interaction with DNA.
  Ann N Y Acad Sci, 758, 143-160.  
  8575189 A.M.Gronenborn, and G.M.Clore (1995).
Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy.
  Crit Rev Biochem Mol Biol, 30, 351-385.  
7625727 B.M.Forman, and R.M.Evans (1995).
Nuclear hormone receptors activate direct, inverted, and everted repeats.
  Ann N Y Acad Sci, 761, 29-37.  
7622518 C.C.Nelson, S.C.Hendy, and P.J.Romaniuk (1995).
Relationship between P-box amino acid sequence and DNA binding specificity of the thyroid hormone receptor. The effects of half-site sequence in everted repeats.
  J Biol Chem, 270, 16981-16987.  
7622519 C.C.Nelson, S.C.Hendy, and P.J.Romaniuk (1995).
Relationship between P-box amino acid sequence and DNA binding specificity of the thyroid hormone receptor. The effects of sequences flanking half-sites in thyroid hormone response elements.
  J Biol Chem, 270, 16988-16994.  
  11725045 Cheng Sy (1995).
New Insights into the Structure and Function of the Thyroid Hormone Receptor.
  J Biomed Sci, 2, 77-89.  
8521508 D.J.Mangelsdorf, and R.M.Evans (1995).
The RXR heterodimers and orphan receptors.
  Cell, 83, 841-850.  
7664096 D.T.Gewirth, and P.B.Sigler (1995).
The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex.
  Nat Struct Biol, 2, 386-394.
PDB code: 1lat
  8593870 G.M.Stancel, H.L.Boettger-Tong, C.Chiappetta, S.M.Hyder, J.L.Kirkland, L.Murthy, and D.S.Loose-Mitchell (1995).
Toxicity of endogenous and environmental estrogens: what is the role of elemental interactions?
  Environ Health Perspect, 103, 29-33.  
7601148 H.Baumann, and T.Härd (1995).
Structural characterization of a short peptide fragment that mediates estrogen-receptor dimerization.
  Eur J Biochem, 230, 879-885.  
7635163 H.H.Thole, I.Maschler, and P.W.Jungblut (1995).
Surface mapping of the ligand-filled C-terminal half of the porcine estradiol receptor by restricted proteolysis.
  Eur J Biochem, 231, 510-516.  
  7651396 H.P.Harding, and M.A.Lazar (1995).
The monomer-binding orphan receptor Rev-Erb represses transcription as a dimer on a novel direct repeat.
  Mol Cell Biol, 15, 4791-4802.  
7559612 J.A.Lupisella, J.E.Driscoll, W.J.Metzler, and P.R.Reczek (1995).
The ligand binding domain of the human retinoic acid receptor gamma is predominantly alpha-helical with a Trp residue in the ligand binding site.
  J Biol Chem, 270, 24884-24890.  
7501014 J.P.Renaud, N.Rochel, M.Ruff, V.Vivat, P.Chambon, H.Gronemeyer, and D.Moras (1995).
Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid.
  Nature, 378, 681-689.
PDB code: 2lbd
  7735836 J.W.Schwabe, L.Chapman, and D.Rhodes (1995).
The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.
  Structure, 3, 201-213.  
7716169 J.Zilliacus, A.P.Wright, J.Carlstedt-Duke, L.Nilsson, and J.A.Gustafsson (1995).
Modulation of DNA-binding specificity within the nuclear receptor family by substitutions at a single amino acid position.
  Proteins, 21, 57-67.  
  7823947 L.D.McBroom, G.Flock, and V.Giguère (1995).
The nonconserved hinge region and distinct amino-terminal domains of the ROR alpha orphan nuclear receptor isoforms are required for proper DNA bending and ROR alpha-DNA interactions.
  Mol Cell Biol, 15, 796-808.  
7696496 M.A.Eriksson, T.Härd, and L.Nilsson (1995).
Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution.
  Biophys J, 68, 402-426.  
8579895 M.R.Haussler, P.W.Jurutka, J.C.Hsieh, P.D.Thompson, S.H.Selznick, C.A.Haussler, and G.K.Whitfield (1995).
New understanding of the molecular mechanism of receptor-mediated genomic actions of the vitamin D hormone.
  Bone, 17, 33S-38S.  
8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.
  Proteins, 23, 525-535.  
7664086 N.D.Arbuckle, and B.Luisi (1995).
A recipe for specificity.
  Nat Struct Biol, 2, 341-346.  
7501015 R.L.Wagner, J.W.Apriletti, M.E.McGrath, B.L.West, J.D.Baxter, and R.J.Fletterick (1995).
A structural role for hormone in the thyroid hormone receptor.
  Nature, 378, 690-697.  
  7565738 S.Kato, H.Sasaki, M.Suzawa, S.Masushige, L.Tora, P.Chambon, and H.Gronemeyer (1995).
Widely spaced, directly repeated PuGGTCA elements act as promiscuous enhancers for different classes of nuclear receptors.
  Mol Cell Biol, 15, 5858-5867.  
7589783 S.M.Hyder, G.L.Shipley, and G.M.Stancel (1995).
Estrogen action in target cells: selective requirements for activation of different hormone response elements.
  Mol Cell Endocrinol, 112, 35-43.  
  7739535 V.Giguère, L.D.McBroom, and G.Flock (1995).
Determinants of target gene specificity for ROR alpha 1: monomeric DNA binding by an orphan nuclear receptor.
  Mol Cell Biol, 15, 2517-2526.  
7828346 A.R.Rut, M.Hewison, K.Kristjansson, B.Luisi, M.R.Hughes, and J.L.O'Riordan (1994).
Two mutations causing vitamin D resistant rickets: modelling on the basis of steroid hormone receptor DNA-binding domain crystal structures.
  Clin Endocrinol (Oxf), 41, 581-590.  
  8137826 C.Zechel, X.Q.Shen, J.Y.Chen, Z.P.Chen, P.Chambon, and H.Gronemeyer (1994).
The dimerization interfaces formed between the DNA binding domains of RXR, RAR and TR determine the binding specificity and polarity of the full-length receptors to direct repeats.
  EMBO J, 13, 1425-1433.  
  8137825 C.Zechel, X.Q.Shen, P.Chambon, and H.Gronemeyer (1994).
Dimerization interfaces formed between the DNA binding domains determine the cooperative binding of RXR/RAR and RXR/TR heterodimers to DR5 and DR4 elements.
  EMBO J, 13, 1414-1424.  
  8168495 F.Bouillaud, I.Arechaga, P.X.Petit, S.Raimbault, C.Levi-Meyrueis, L.Casteilla, M.Laurent, E.Rial, and D.Ricquier (1994).
A sequence related to a DNA recognition element is essential for the inhibition by nucleotides of proton transport through the mitochondrial uncoupling protein.
  EMBO J, 13, 1990-1997.  
  8019409 G.M.Clore, and A.M.Gronenborn (1994).
Young Investigator Award Lecture. Structures of larger proteins, protein-ligand and protein-DNA complexes by multidimensional heteronuclear NMR.
  Protein Sci, 3, 372-390.  
7664042 J.W.Schwabe, and A.Klug (1994).
Zinc mining for protein domains.
  Nat Struct Biol, 1, 345-349.  
7925381 M.S.Lee, D.S.Sem, S.A.Kliewer, J.Provencal, R.M.Evans, and P.E.Wright (1994).
NMR assignments and secondary structure of the retinoid X receptor alpha DNA-binding domain. Evidence for the novel C-terminal helix.
  Eur J Biochem, 224, 639-650.  
7809040 M.Suzuki, and N.Yagi (1994).
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
  Proc Natl Acad Sci U S A, 91, 12357-12361.  
  8087558 M.Suzuki (1994).
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
  Structure, 2, 317-326.  
8001144 P.Sengupta, H.A.Colbert, and C.I.Bargmann (1994).
The C. elegans gene odr-7 encodes an olfactory-specific member of the nuclear receptor superfamily.
  Cell, 79, 971-980.  
  16100953 J.W.Schwabe, L.Chapman, J.T.Finch, D.Rhodes, and D.Neuhaus (1993).
DNA recognition by the oestrogen receptor: from solution to the crystal.
  Structure, 1, 187-204.
PDB code: 1hcp
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.