[English] 日本語
Yorodumi- PDB-1gwr: HUMAN OESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gwr | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN OESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX WITH 17BETA-OESTRADIOL AND TIF2 NRBOX3 PEPTIDE | ||||||
Components |
| ||||||
Keywords | NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / TRANSACTIVATION / AGONIST / AF2 COACTIVATOR / RECEPTOR / ACTIVATOR / TRANSCRIPTI REGULATION / DNA-BINDING / NUCLEAR PROTEIN / ZINC FINGER / STER BINDING / PHOSPHORYLATION / POLYMORPHISM / ALTERNATIVE SPLICING | ||||||
Function / homology | Function and homology information 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 ...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 / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / 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 / Recycling of bile acids and salts / 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 / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / 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 receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / 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 / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / fibroblast proliferation / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Pike, A.C.W. / Brzozowski, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Interaction of Transcriptional Intermediary Factor 2 Nuclear Receptor Box Peptides with the Coactivator Binding Site of Estrogen Receptor Alpha. Authors: Warnmark, A. / Treuter, E. / Gustafsson, J.-A. / Hubbard, R.E. / Brzozowski, A.M. / Pike, A.C.W. #1: Journal: Nature / Year: 1997 Title: Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor Authors: Brzozowski, A.M. / Pike, A.C. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustafsson, J.A. / Carlquist, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gwr.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gwr.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gwr_validation.pdf.gz | 832.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gwr_full_validation.pdf.gz | 784.7 KB | Display | |
Data in XML | 1gwr_validation.xml.gz | 18 KB | Display | |
Data in CIF | 1gwr_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/1gwr ftp://data.pdbj.org/pub/pdb/validation_reports/gw/1gwr | HTTPS FTP |
-Related structure data
Related structure data | 1gwqC 1ereS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.7615, 0.07627, 0.64366), Vector: |
-Components
#1: Protein | Mass: 28022.037 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN RESIDUES 305-549 Source method: isolated from a genetically manipulated source Details: LIGAND-BINDING DOMAIN (DOMAIN E - RESIDUES 260-500) IN COMPLEX WITH THE AGONIST 17BETA-OESTRADIOL Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEALPHA 35 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): C1857 / References: UniProt: P03372 #2: Protein/peptide | Mass: 1091.282 Da / Num. of mol.: 2 / Fragment: NUCLEAR RECEPTOR BOX III RESIDUES 742-750 / Source method: obtained synthetically Details: TIF2 NR-BOX REGION 3 DERIVED PEPTIDE (RESIDUES 740-751) Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15596 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.5 % |
---|---|
Crystal grow | pH: 7.8 / Details: 2-2.5% (W/V) PEG 20000 0.1M HEPES PH7.8, pH 7.80 |
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 20680 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2 / % possible all: 82.9 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 134819 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 82.9 % / Num. unique obs: 915 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ERE Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.584 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: METHOD USED: BULK SOLVENT CONTRIBUTIONS CALCULATED BY XPLOR WERE INCORPORATE IN THE FORM OF PARTIAL STRUCTURE FACTORS
| ||||||||||||||||||||
Displacement parameters | Biso mean: 41.3 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.52 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.404 Å / Lowest resolution: 2.518 Å / Num. reflection Rwork: 2289 |