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- PDB-2gpv: Estrogen Related Receptor-gamma ligand binding domain complexed w... -
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Open data
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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 | ||||||
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![]() | TRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor / SMRT / Tamoxifen | ||||||
Function / homology | ![]() 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 / nuclear receptor-mediated steroid hormone signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / lactation / transcription repressor complex / steroid binding / Regulation of lipid metabolism by PPARalpha / 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 / Nuclear Receptor transcription pathway / HCMV Early Events / 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 / regulation of DNA-templated transcription / chromatin / 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 / identical protein binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.7 KB | Display | ![]() |
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PDB format | ![]() | 218.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 47 KB | Display | |
Data in CIF | ![]() | 62.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gp7SC ![]() 2gpoC ![]() 2gppC ![]() 2gpuC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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