[English] 日本語
Yorodumi- PDB-1a52: ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN COMPLEXED TO ESTRADIOL -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a52 | ||||||
---|---|---|---|---|---|---|---|
Title | ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN COMPLEXED TO ESTRADIOL | ||||||
Components | ESTROGEN RECEPTOR | ||||||
Keywords | RECEPTOR / ESTROGEN / LIGAND / TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / nuclear estrogen receptor binding / stem cell differentiation / positive regulation of nitric-oxide synthase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Tanenbaum, D.M. / Wang, Y. / Sigler, P.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains. Authors: Tanenbaum, D.M. / Wang, Y. / Williams, S.P. / Sigler, P.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a52.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a52.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a52 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a52 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 |
| |||||||||||||||
3 |
| |||||||||||||||
4 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (-0.966537, -0.255999, 0.016449), Vector: |
-Components
#1: Protein | Mass: 29507.809 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: ESR / Plasmid: PET223D / Gene (production host): ERG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLSS / References: UniProt: P03372 #2: Chemical | #3: Chemical | ChemComp-AU / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.65 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: WELL: 100 MM TRIS PH 7.6 480 MM MGCL2 10 MM MGOAC2 10% ETHYLENE GLYCOL 5% PEG 4000. PROTEIN STOCK: 18 MG/ML ERLBD 25 MM TRIS PH 7.4 200 MM NACL 1 MM EDTA 1 MM DTT 20 MICROMOLAR ESTRADIOL 0. ...Details: WELL: 100 MM TRIS PH 7.6 480 MM MGCL2 10 MM MGOAC2 10% ETHYLENE GLYCOL 5% PEG 4000. PROTEIN STOCK: 18 MG/ML ERLBD 25 MM TRIS PH 7.4 200 MM NACL 1 MM EDTA 1 MM DTT 20 MICROMOLAR ESTRADIOL 0.1% BETA-OCTYL GLUCOSIDE AT 18 CELSIUS., vapor diffusion - hanging drop, temperature 291K PH range: 7.4-7.6 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0397 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: SPHERICAL MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0397 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 33401 / % possible obs: 99.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.075 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.329 / % possible all: 98.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.8→50 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: DENSITY MODIFICATION / Bsol: -9999 Å2 / ksol: 999 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.83 Å / Total num. of bins used: 30
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS DEVELOPMENT / Version: VERSION 0.3A / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.4322 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|