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Yorodumi- PDB-1l2i: Human Estrogen Receptor alpha Ligand-binding Domain in Complex wi... -
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-Basic information
Entry | Database: PDB / ID: 1l2i | ||||||
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Title | Human Estrogen Receptor alpha Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol and a Glucocorticoid Receptor Interacting Protein 1 NR box II Peptide | ||||||
Components |
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Keywords | TRANSCRIPTION RECEPTOR/COACTIVATOR / nuclear receptor / transcription factor / estrogen / agonist / coactivator / TRANSCRIPTION RECEPTOR-COACTIVATOR COMPLEX | ||||||
Function / homology | Function and homology information Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 ...Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / 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 / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / 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 / 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 / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / 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 / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / circadian rhythm / 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 / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Shiau, A.K. / Barstad, D. / Radek, J.T. / Meyers, M.J. / Nettles, K.W. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Agard, D.A. / Greene, G.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism. Authors: Shiau, A.K. / Barstad, D. / Radek, J.T. / Meyers, M.J. / Nettles, K.W. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Agard, D.A. / Greene, G.L. #1: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of this Interaction by Tamoxifen Authors: Shiau, A.K. / Barstad, D. / Loria, P.M. / Cheng, L. / Kushner, P.J. / Agard, D.A. / Greene, G.L. #2: Journal: J.Med.Chem. / Year: 1999 Title: Estrogen Receptor Subtype-selective Ligands: Asymmetric Synthesis and Biological Evaluation of cis- and trans-5,11-dialkyl-5,6,11,12-tetrahydrochrysenes Authors: Meyers, M.J. / Sun, J. / Carlson, K.E. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l2i.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l2i.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 1l2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l2i_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1l2i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1l2i_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1l2i_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/1l2i ftp://data.pdbj.org/pub/pdb/validation_reports/l2/1l2i | HTTPS FTP |
-Related structure data
Related structure data | 1l2jC 3erdS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29908.256 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (residues 297-554) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET23D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P03372 #2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 2 / Fragment: NR box II (residues 686-698) / Source method: obtained synthetically Details: The peptide was chemically synthesized. This sequence occurs naturally in mice. References: UniProt: Q61026 #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 1.96 Å3/Da / Density % sol: 43.48 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 16% (w/v) PEG 4000, 50 mM Magnesium chloride, 53 mM Tris pH 8.8 292-294 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19-21 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 1999 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.8 Å / Num. all: 34533 / Num. obs: 34533 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.065 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 3432 / Rsym value: 0.531 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 119409 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.531 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ERD Resolution: 1.95→46.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 61.9288 Å2 / ksol: 0.360796 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→46.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.203 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.336 / Rfactor Rwork: 0.296 / Rfactor obs: 0.296 |