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- PDB-2qa6: Crystal Structure of Estrogen Receptor Alpha mutant 537S Complexe... -
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Basic information
Entry | Database: PDB / ID: 2qa6 | ||||||
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Title | Crystal Structure of Estrogen Receptor Alpha mutant 537S Complexed with 4-(6-hydroxy-1H-indazol-3-yl)benzene-1,3-diol | ||||||
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![]() | TRANSCRIPTION / Protein-Ligand Complex | ||||||
Function / homology | ![]() 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 / Estrogen-dependent gene expression / nuclear glucocorticoid receptor binding / 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 / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / DNA polymerase binding / nuclear retinoid X receptor 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 / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / circadian rhythm / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.8 KB | Display | ![]() |
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PDB format | ![]() | 86.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 481.1 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b23C ![]() 2qa8C ![]() 2qabC ![]() 2qgtC ![]() 2qgwC ![]() 2qh6C ![]() 2qr9C ![]() 2qseC ![]() 2qxmC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Details: Flat mirror (vertical focusing) |
Radiation | Monochromator: single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 14355 / Num. obs: 14355 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 67.702 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Χ2: 1.545 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.35 / Num. unique all: 1044 / Rsym value: 0.535 / Χ2: 1.612 / % possible all: 67.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.666 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 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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