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Open data
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Basic information
Entry | Database: PDB / ID: 6fo7 | |||||||||
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Title | Vitamin D nuclear receptor complex 3 | |||||||||
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![]() | GENE REGULATION | |||||||||
Function / homology | ![]() heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / vitamin D response element binding / lithocholic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / vitamin D response element binding / lithocholic acid binding / 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 / hematopoietic stem cell proliferation / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / heart looping / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / calcium ion homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / 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 / Regulation of lipid metabolism by PPARalpha / ossification / 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 / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rochel, N. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Aromatic-Based Design of Highly Active and Noncalcemic Vitamin D Receptor Agonists. Authors: Gogoi, P. / Seoane, S. / Sigueiro, R. / Guiberteau, T. / Maestro, M.A. / Perez-Fernandez, R. / Rochel, N. / Mourino, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.5 KB | Display | ![]() |
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PDB format | ![]() | 92.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.5 KB | Display | ![]() |
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Full document | ![]() | 710.1 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fo8C ![]() 6fo9C ![]() 6fobC ![]() 6fodC ![]() 2hc4S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33916.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q9PTN2 |
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#2: Protein/peptide | Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-LX3 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0721 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→25 Å / Num. obs: 11375 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 66.88 Å2 / Rsym value: 0.107 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.59→2.69 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HC4 Resolution: 2.59→23.33 Å / Cor.coef. Fo:Fc: 0.9189 / Cor.coef. Fo:Fc free: 0.9123 / SU R Cruickshank DPI: 0.391 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.48 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.255
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Displacement parameters | Biso mean: 81.36 Å2
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Refine analyze | Luzzati coordinate error obs: 0.392 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.59→23.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.84 Å / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 8.3682 Å / Origin y: 38.1371 Å / Origin z: 42.1786 Å
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Refinement TLS group | Selection details: { A|* } |