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Yorodumi- PDB-2qh6: Crystal Structure of the Estrogen Receptor Alpha Ligand Binding D... -
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-Basic information
Entry | Database: PDB / ID: 2qh6 | ||||||
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Title | Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with an Oxabicyclic diarylethylene Compound | ||||||
Components |
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Keywords | TRANSCRIPTION / Protein-Ligand Complex | ||||||
Function / homology | Function and homology information Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 ...Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / nuclear glucocorticoid receptor binding / Estrogen-dependent gene expression / nuclear retinoic acid receptor binding / positive regulation of female receptivity / nuclear thyroid hormone receptor binding / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / nuclear retinoid X receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / mammary gland alveolus development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / estrogen receptor signaling pathway / cellular response to estrogen stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / estrogen response element binding / : / regulation of cellular response to insulin stimulus / DNA polymerase binding / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / negative regulation of miRNA transcription / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / Nuclear Receptor transcription pathway / circadian rhythm / euchromatin / negative regulation of DNA-binding transcription factor activity / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / regulation of inflammatory response / response to estradiol / ATPase binding / regulation of gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Nettles, K.W. / Bruning, J.B. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Shi, Y. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. ...Nettles, K.W. / Bruning, J.B. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Shi, Y. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. / Katzenellenbogen, B.S. / Kim, Y. / Joachmiak, A. / Greene, G.L. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2008 Title: NFkappaB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses Authors: Nettles, K.W. / Bruning, J.B. / Gil, G. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. / Katzenellenbogen, B.S. / Kim, Y. / Joachmiak, A. / Greene, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qh6.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qh6.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qh6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2qh6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2qh6_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 2qh6_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/2qh6 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/2qh6 | HTTPS FTP |
-Related structure data
Related structure data | 2b23C 2qa6C 2qa8C 2qabC 2qgtC 2qgwC 2qr9C 2qseC 2qxmC 3erdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29386.609 Da / Num. of mol.: 2 / Fragment: Steroid-binding region, residues 298-554 / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P03372 #2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8BN74, UniProt: Q61026*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9734 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2004 / Details: bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: bent cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9734 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 13294 / Num. obs: 13294 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.36 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Χ2: 2.933 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.47 / Num. unique all: 1332 / Rsym value: 0.546 / Χ2: 2.078 / % possible all: 98.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3ERD Resolution: 2.7→19.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.856 / SU B: 33.042 / SU ML: 0.315 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.364 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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