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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 / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / 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 / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / 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 / 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 / : / 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 / 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 / cerebellum development / 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 estrogen receptor binding / nuclear 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 / circadian rhythm / response to estrogen / RNA polymerase II transcription regulator complex 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
Summary document | 3l03_validation.pdf.gz | 981.8 KB | Display | wwPDB validaton report |
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Full document | 3l03_full_validation.pdf.gz | 991.9 KB | Display | |
Data in XML | 3l03_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3l03_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/3l03 ftp://data.pdbj.org/pub/pdb/validation_reports/l0/3l03 | HTTPS FTP |
-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 |