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Yorodumi- PDB-3l03: Crystal Structure of human Estrogen Receptor alpha Ligand-Binding... -
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-Basic information
Entry | Database: PDB / ID: 3l03 | ||||||
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Title | Crystal Structure of human Estrogen Receptor alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II peptide and Estetrol (Estra-1,3,5(10)-triene-3,15 alpha,16alpha,17beta-tetrol) | ||||||
Components |
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Keywords | TRANSCRIPTION / estrogen receptor / LBD / GRIP peptide / estetrol / DNA-binding / Glycoprotein / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Receptor / Steroid-binding / Transcription regulation / Zinc-finger / Activator | ||||||
Function / homology | Function and homology information HATs acetylate histones / Endogenous sterols / Synthesis of bile acids and bile salts / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Regulation of lipid metabolism by PPARalpha / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of glucocorticoid receptor signaling pathway / Cytoprotection by HMOX1 ...HATs acetylate histones / Endogenous sterols / Synthesis of bile acids and bile salts / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Regulation of lipid metabolism by PPARalpha / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of glucocorticoid receptor signaling pathway / Cytoprotection by HMOX1 / 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 / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / androgen metabolic process / TFIIB-class transcription factor binding / regulation of lipid metabolic process / steroid hormone mediated signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of phospholipase C activity / DNA polymerase binding / nuclear retinoid X receptor binding / intracellular steroid hormone receptor 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 / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / Regulation of lipid metabolism by PPARalpha / nitric-oxide synthase regulator activity / cerebellum development / ESR-mediated signaling / 14-3-3 protein binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / negative regulation of miRNA transcription / response to progesterone / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / positive regulation of nitric-oxide synthase activity / circadian regulation of gene expression / Heme signaling / euchromatin / SUMOylation of intracellular receptors / 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 / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / circadian rhythm / response to estrogen / RNA polymerase II transcription regulator complex / male gonad development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å | ||||||
Authors | Rajan, S.S. / Kim, Y. / Vanek, K. / Joachimiak, A. / Greene, G.L. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of human Estrogen Receptor alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II peptide and Estra-1,3,5(10)-triene-3,15 ...Title: Crystal Structure of human Estrogen Receptor alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II peptide and Estra-1,3,5(10)-triene-3,15 alpha,16alpha,17beta-tetrol Authors: Rajan, S.S. / Kim, Y. / Vanek, K. / Joachimiak, 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 | 3l03.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l03.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 3l03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/3l03 ftp://data.pdbj.org/pub/pdb/validation_reports/l0/3l03 | HTTPS FTP |
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-Related structure data
Related structure data | 1zkyS 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
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 29019.279 Da / Num. of mol.: 2 / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: MCSG7 (pET12-derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372 #2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596, UniProt: Q9WUI9*PLUS |
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-Non-polymers , 4 types, 136 molecules
#3: Chemical | ChemComp-CL / | ||
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#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | SOME OF THE CYS RESIDUES WERE OXIDIZED TO CME. THE AUTHORS WERE ONLY ABLE TO DETECT CME AT POSITION ...SOME OF THE CYS RESIDUES WERE OXIDIZED TO CME. THE AUTHORS WERE ONLY ABLE TO DETECT CME AT POSITION 530 FROM THE ELECTRON DENSITY MAP. |
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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: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15% (v/v) ethanol, HEPES pH 7.5, MgCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2009 / Details: mirrors |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.896→50 Å / Num. all: 40926 / Num. obs: 40149 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 29.52 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 39.365 |
Reflection shell | Resolution: 1.896→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 1636 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDb entry 1ZKY Resolution: 1.896→32.954 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.702 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.896→32.954 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain D |