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- PDB-4g1z: Structural basis for the accommodation of bis- and tris-aromatic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4g1z | ||||||
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Title | Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor | ||||||
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![]() | transcription/transcription inhibitor / VDR / nuclear receptor / transcription regulation / alpha helical sandwich / ligand / DNA / phosphorylation / nucleus / transcription-transcription inhibitor complex | ||||||
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 / chromatin / regulation of DNA-templated transcription / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ciesielski, F. / Sato, Y. / Moras, D. / Rochel, N. | ||||||
![]() | ![]() Title: Structural basis for the accommodation of bis- and tris-aromatic derivatives in vitamin d nuclear receptor. Authors: Ciesielski, F. / Sato, Y. / Chebaro, Y. / Moras, D. / Dejaegere, A. / Rochel, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
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PDB format | ![]() | 46.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 720.3 KB | Display | ![]() |
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Full document | ![]() | 729 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g1dC ![]() 4g1yC ![]() 4g20C ![]() 4g21C ![]() 4g2hC ![]() 4g2iC 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 / Fragment: unp residues 156-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1776.072 Da / Num. of mol.: 1 / Fragment: unp residues 686-692 / Source method: obtained synthetically / Details: from human sequence / Source: (synth.) ![]() |
#3: Chemical | ChemComp-0VP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 14308 / % possible obs: 85.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.5→2.57 Å / % possible all: 81.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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