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Yorodumi- PDB-2gpu: Estrogen Related Receptor-gamma ligand binding domain complexed w... -
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-Basic information
Entry | Database: PDB / ID: 2gpu | ||||||
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Title | Estrogen Related Receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen | ||||||
Components | Estrogen-related receptor gamma | ||||||
Keywords | TRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor | ||||||
Function / homology | Function and homology information AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis ...AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 2gpu.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gpu.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gpu_validation.pdf.gz | 720.2 KB | Display | wwPDB validaton report |
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Full document | 2gpu_full_validation.pdf.gz | 724.6 KB | Display | |
Data in XML | 2gpu_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 2gpu_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/2gpu ftp://data.pdbj.org/pub/pdb/validation_reports/gp/2gpu | HTTPS FTP |
-Related structure data
Related structure data | 2gp7SC 2gpoC 2gppC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26084.373 Da / Num. of mol.: 1 / 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 |
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#2: Chemical | ChemComp-OHT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 36% Peg600, 0.1M tris, 0.1% zwittergent 3-16, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-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: 1.7→50 Å / Num. all: 32660 / Num. obs: 32333 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Rmerge(I) obs: 0.07 / Χ2: 0.997 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GP7 Resolution: 1.7→46.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.857 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.092 / 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: 21.881 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→46.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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