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Yorodumi- PDB-2gpp: Estrogen Related Receptor-gamma ligand binding domain complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gpp | ||||||
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Title | Estrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716 | ||||||
Components |
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Keywords | TRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor / RIP140 | ||||||
Function / homology | Function and homology information ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear steroid receptor activity / histone deacetylase complex / retinoic acid receptor signaling pathway / estrogen response element binding ...ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear steroid receptor activity / histone deacetylase complex / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / steroid binding / SUMOylation of transcription cofactors / cellular response to estradiol stimulus / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / fibrillar center / histone deacetylase binding / Nuclear Receptor transcription pathway / circadian rhythm / nuclear receptor activity / transcription corepressor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Circadian Clock / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 2gpp.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gpp.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gpp_validation.pdf.gz | 669.8 KB | Display | wwPDB validaton report |
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Full document | 2gpp_full_validation.pdf.gz | 671.2 KB | Display | |
Data in XML | 2gpp_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2gpp_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/2gpp ftp://data.pdbj.org/pub/pdb/validation_reports/gp/2gpp | HTTPS FTP |
-Related structure data
Related structure data | 2gp7SC 2gpoC 2gpuC 2gpvC 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: Component-ID: 1 / Refine code: 5
NCS ensembles :
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-Components
#1: Protein | Mass: 26084.373 Da / Num. of mol.: 2 / Fragment: 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: 2833.291 Da / Num. of mol.: 2 / Fragment: Residues (366-390) / Source method: obtained synthetically Details: Chemically synthesized. Occurs naturally in Humans. References: UniProt: P48552 #3: Chemical | ChemComp-1BA / | #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: 3.69 Å3/Da / Density % sol: 66.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 9% PEG 20K 0.1M MES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 295K |
-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: 2.6→50 Å / Num. all: 25371 / Num. obs: 25066 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.064 / Χ2: 1.029 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GP7 Resolution: 2.6→45.74 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.449 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.269 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.602 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→45.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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