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Yorodumi- PDB-2jfa: ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH AN AFFINITY-SELECTED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jfa | ||||||
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Title | ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH AN AFFINITY-SELECTED COREPRESSOR PEPTIDE | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / PHAGE DISPLAY / METAL-BINDING / COREPRESSOR / LIPID-BINDING / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN (LBD) / NUCLEAR PROTEIN / PHOSPHORYLATION / STEROID- BINDING / RECEPTOR / ZINC-FINGER / DNA-BINDING / NUCLEAR RECEPTOR / PEPTIDE ANTAGONIST | ||||||
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 / 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 / protein localization to chromatin / 14-3-3 protein binding / 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 / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / euchromatin / 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 / response to estrogen / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / 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 DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / 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: 2.55 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 | 2jfa.cif.gz | 112.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jfa.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jfa_validation.pdf.gz | 974 KB | Display | wwPDB validaton report |
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Full document | 2jfa_full_validation.pdf.gz | 990.8 KB | Display | |
Data in XML | 2jfa_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 2jfa_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jfa ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jfa | HTTPS FTP |
-Related structure data
Related structure data | 2jf9C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 28672.541 Da / Num. of mol.: 1 / 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 |
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#2: Protein | Mass: 28730.576 Da / Num. of mol.: 1 / 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 |
-Protein/peptide , 1 types, 2 molecules PQ
#3: Protein/peptide | Mass: 1903.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: BT1 PEPTIDE / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 3 types, 92 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: 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: 4.6 Å3/Da / Density % sol: 73.1 % |
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Crystal grow | pH: 5.6 Details: 0.35M AMMONIUM SULPHATE, 0.7M LITHIUM SULPHATE, 0.07M TRI-SODIUM CITRATE PH5.6, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 34500 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 59.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BJ4 Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.1 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.191 / 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: 42.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→30 Å
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Refine LS restraints |
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