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Yorodumi- PDB-2b1v: Human estrogen receptor alpha ligand-binding domain in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 2b1v | ||||||
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Title | Human estrogen receptor alpha ligand-binding domain in complex with OBCP-1M and a glucocorticoid receptor interacting protein 1 NR box II peptide | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR RECEPTOR / ESTROGEN RECEPTOR / LBD / GRIP PEPTIDE / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
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 / 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 ...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 / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Nuclear signaling by ERBB4 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / 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 / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / SUMOylation of transcription cofactors / 14-3-3 protein binding / Activation of gene expression by SREBF (SREBP) / transcription corepressor binding / negative regulation of miRNA transcription / response to progesterone / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / nuclear receptor binding / circadian regulation of gene expression / euchromatin / Heme signaling / 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 / response to estrogen / RNA polymerase II transcription regulator complex / male gonad development / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / 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 / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Rajan, S.S. / Hsieh, R.W. / Sharma, S.K. / Greene, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Identification of ligands with bicyclic scaffolds provides insights into mechanisms of estrogen receptor subtype selectivity. Authors: Hsieh, R.W. / Rajan, S.S. / Sharma, S.K. / Guo, Y. / Desombre, E.R. / Mrksich, M. / 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 | 2b1v.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b1v.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 2b1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/2b1v ftp://data.pdbj.org/pub/pdb/validation_reports/b1/2b1v | HTTPS FTP |
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-Related structure data
Related structure data | 1zkySC 2faiC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 29527.887 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: MCSG7 (PET12-DERIVATIVE) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P03372 #2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 2 / Fragment: RESIDUES 686 - 698 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. / References: UniProt: Q15596 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 135 / Detector: CCD / Date: Aug 9, 2005 / Details: Bent conical Si-mirror (Rh coated) |
Radiation | Monochromator: Bent Ge(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 46440 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.053 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.73 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZKY Resolution: 1.8→19.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.504 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.484 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.803→1.85 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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