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Yorodumi- PDB-2gpv: Estrogen Related Receptor-gamma ligand binding domain complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gpv | ||||||
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Title | Estrogen Related Receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen and a SMRT peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor / SMRT / Tamoxifen | ||||||
Function / homology | Function and homology information AF-2 domain binding / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity ...AF-2 domain binding / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / estrous cycle / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / lactation / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / steroid binding / cerebellum development / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / response to estradiol / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Wang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Osband-miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: X-ray crystal structures of the estrogen-related receptor-gamma ligand binding domain in three functional states reveal the molecular basis of small molecule regulation. Authors: Wang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Orband-Miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gpv.cif.gz | 267.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gpv.ent.gz | 218.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/2gpv ftp://data.pdbj.org/pub/pdb/validation_reports/gp/2gpv | HTTPS FTP |
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-Related structure data
Related structure data | 2gp7SC 2gpoC 2gppC 2gpuC 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 domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
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-Components
#1: Protein | Mass: 26084.373 Da / Num. of mol.: 6 / Fragment: Ligand Binding Domain (residues 229-458) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62508 #2: Protein/peptide | Mass: 2599.999 Da / Num. of mol.: 3 / Fragment: LXXLL Motif (residues 2338-2359) / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: Q9Y618, UniProt: Q4RA23*PLUS #3: Chemical | ChemComp-OHT / #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: 3.15 Å3/Da / Density % sol: 60.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 7% PEG3350 0.2M Lithium Acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. all: 48079 / Num. obs: 43368 / % possible obs: 90.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Χ2: 1.018 |
Reflection shell | Resolution: 2.85→2.95 Å / % possible obs: 39.9 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.298 / Num. measured obs: 1891 / Χ2: 0.86 / % possible all: 38.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GP7 Resolution: 2.85→19.91 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.819 / SU B: 34.341 / SU ML: 0.319 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / 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: 13.974 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→19.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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