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- PDB-1kv6: X-ray structure of the orphan nuclear receptor ERR3 ligand-bindin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kv6 | ||||||
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Title | X-ray structure of the orphan nuclear receptor ERR3 ligand-binding domain in the constitutively active conformation | ||||||
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![]() | GENE REGULATION / transcriptionally active conformation in absence of ligand / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | ![]() regulation of cellular response to drug / nuclear progesterone receptor binding / nuclear receptor binding => GO:0016922 / : / AF-2 domain binding / : / chromatin => GO:0000785 / bile acid and bile salt transport / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway ...regulation of cellular response to drug / nuclear progesterone receptor binding / nuclear receptor binding => GO:0016922 / : / AF-2 domain binding / : / chromatin => GO:0000785 / bile acid and bile salt transport / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / steroid binding / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / positive regulation of cold-induced thermogenesis / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / neuron projection / positive regulation of apoptotic process / chromatin binding / protein-containing complex binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Greschik, H. / Wurtz, J.-M. / Sanglier, S. / Bourguet, W. / van Dorsselaer, A. / Moras, D. / Renaud, J.-P. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: Structural and Functional Evidence for Ligand-Independent Transcriptional Activation by the Estrogen-Related Receptor 3 Authors: Greschik, H. / Wurtz, J.-M. / Sanglier, S. / Bourguet, W. / van Dorsselaer, A. / Moras, D. / Renaud, J.-P. #1: ![]() Title: Molecular basis of agonism and antagonism in the oestrogen receptor Authors: Brzozowski, A.M. / Pike, A.C. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustafsson, J.A. #2: ![]() Title: The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction with tamoxifen Authors: Shiau, A.K. / Barstad, D. / Loria, P.M. / Cheng, L. / Agard, D.A. / Greene, G.L. #3: ![]() Title: X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation Authors: Stehlin, C. / Wurtz, J.M. / Steinmetz, A. / Greiner, E. / Schuele, R. / Moras, D. / Renaud, J.P. #4: ![]() Title: Structural studies on nuclear receptors Authors: Renaud, J.P. / Moras, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 450.2 KB | Display | ![]() |
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Full document | ![]() | 464.7 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3erdS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26084.373 Da / Num. of mol.: 2 / Fragment: ligand-binding domain Source method: isolated from a genetically manipulated source Details: complex with a SRC1 coactivator peptide in the absence of ligand Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1776.072 Da / Num. of mol.: 2 / Fragment: second NR-box / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q13420, UniProt: Q15788*PLUS #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris.HCl, ammonium sulfate, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2001 / Details: diamond(111) monochromator, Ge(220) focusing |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→15 Å / Num. obs: 23306 / % possible obs: 96.7 % / Biso Wilson estimate: 71 Å2 / Rsym value: 0.049 |
Reflection shell | Resolution: 2.7→2.81 Å / Num. unique all: 2587 / Rsym value: 0.148 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Rmerge(I) obs: 0.148 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PBD ENTRY 3ERD Resolution: 2.7→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.75 Å
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.233 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |