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Yorodumi- PDB-3d24: Crystal structure of ligand-binding domain of estrogen-related re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d24 | ||||||
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Title | Crystal structure of ligand-binding domain of estrogen-related receptor alpha (ERRalpha) in complex with the peroxisome proliferators-activated receptor coactivator-1alpha box3 peptide (PGC-1alpha) | ||||||
Components |
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Keywords | TRANSCRIPTION / nuclear receptor / ligand binding domain / coactivator / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc / Zinc-finger / Polymorphism / RNA-binding / Structural Genomics / Structural Proteomics in Europe / SPINE | ||||||
Function / homology | Function and homology information positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / cellular respiration / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation ...positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / cellular respiration / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / temperature homeostasis / nuclear steroid receptor activity / intercellular bridge / response to starvation / positive regulation of ATP biosynthetic process / response to dietary excess / intracellular glucose homeostasis / fatty acid oxidation / adipose tissue development / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / energy homeostasis / intracellular steroid hormone receptor signaling pathway / brown fat cell differentiation / positive regulation of gluconeogenesis / digestion / respiratory electron transport chain / steroid binding / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / negative regulation of smooth muscle cell proliferation / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PML body / PPARA activates gene expression / chromatin DNA binding / fibrillar center / mRNA processing / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / microtubule cytoskeleton / Circadian Clock / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein domain specific binding / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Moras, D. / Greschik, H. / Flaig, R. / Sato, Y. / Rochel, N. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Communication between the ERR{alpha} Homodimer Interface and the PGC-1{alpha} Binding Surface via the Helix 8-9 Loop. Authors: Greschik, H. / Althage, M. / Flaig, R. / Sato, Y. / Chavant, V. / Peluso-Iltis, C. / Choulier, L. / Cronet, P. / Rochel, N. / Schule, R. / Stromstedt, P.E. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d24.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d24.ent.gz | 81.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d24 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d24 | HTTPS FTP |
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-Related structure data
Related structure data | 1xb7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A HOMODIMER. |
-Components
#1: Protein | Mass: 27584.893 Da / Num. of mol.: 2 / Fragment: Ligand binding domain: Residues 278-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRA, ERR1, ESRL1, NR3B1 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11474 #2: Protein/peptide | Mass: 2665.975 Da / Num. of mol.: 2 / Fragment: Residues 198-219 / Source method: obtained synthetically Details: Synthetic peptide with the sequence based on the fragment (residues 198-219) of human PGC-1-alpha, UniProt entry Q9UBK2 (PRGC1_HUMAN) References: UniProt: Q9UBK2 #3: 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: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 15% PEG 3350, 0.2 M Mg(NO3)2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2007 / Details: Toroidal Zerodur mirror |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→50 Å / Num. all: 111465 / Num. obs: 109542 / % possible obs: 88.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.031 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.11→2.19 Å / Redundancy: 3.2 % / Num. unique all: 2740 / Rsym value: 0.238 / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XB7 Resolution: 2.11→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Bijvoet differences were used in phasing
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Displacement parameters | Biso mean: 42.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→50 Å
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Refine LS restraints |
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