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Yorodumi- PDB-2jf9: ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A TAMOXIFEN-SPECIFIC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jf9 | ||||||
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Title | ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A TAMOXIFEN-SPECIFIC PEPTIDE ANTAGONIST | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / LIPID-BINDING / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN (LBD) / RECEPTOR / ZINC-FINGER / DNA-BINDING / STEROID-BINDING / NUCLEAR RECEPTOR / PEPTIDE ANTAGONIST / METAL-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION | ||||||
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 / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element 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 / negative regulation of miRNA transcription / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / euchromatin / negative regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / transcription regulator complex / Estrogen-dependent gene expression / 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 / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Heldring, N. / Pawson, T. / McDonnell, D. / Treuter, E. / Gustafsson, J.A. / Pike, A.C.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural Insights Into Corepressor Recognition by Antagonist-Bound Estrogen Receptors. Authors: Heldring, N. / Pawson, T. / Mcdonnell, D. / Treuter, E. / Gustafsson, J.A. / Pike, A.C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jf9.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jf9.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jf9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2jf9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2jf9_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 2jf9_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jf9 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jf9 | HTTPS FTP |
-Related structure data
Related structure data | 2jfaC 2bj4S 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein / Protein/peptide , 2 types, 6 molecules ABCPQR
#1: Protein | Mass: 28672.541 Da / Num. of mol.: 3 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 304-533 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P03372 #2: Protein/peptide | Mass: 1541.728 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: PEPTIDE DERIVED FROM PHAGE DISPLAY SCREEN OF RANDOM PEPTIDE LIBRARY Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 5 types, 308 molecules
#3: Chemical | #4: Chemical | ChemComp-BCT / | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: 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: 4.08 Å3/Da / Density % sol: 70 % |
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Crystal grow | pH: 8.5 Details: 2.5% PEG550MME 2.5% PEK20K 0.06M CALCIUM ACETATE 0.1M TRIS PH8.5, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 80788 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BJ4 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.324 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.116 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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