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Yorodumi- PDB-3uvv: Crystal Structure of the ligand binding domains of the thyroid re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uvv | |||||||||
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Title | Crystal Structure of the ligand binding domains of the thyroid receptor:retinoid X receptor complexed with 3,3',5 triiodo-L-thyronine and 9-cis retinoic acid | |||||||||
Components |
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Keywords | HORMONE RECEPTOR/HORMONE RECEPTOR / TR-RXR heterodimer / allostery / alpha helical sandwich / transactivation / HORMONE RECEPTOR-HORMONE RECEPTOR complex | |||||||||
Function / homology | Function and homology information thyroid hormone mediated signaling pathway / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / anatomical structure development ...thyroid hormone mediated signaling pathway / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / anatomical structure development / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / thyroid hormone binding / transcription factor binding / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / Recycling of bile acids and salts / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / signaling receptor activity / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / host cell nucleus / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Fernandez, E.J. / Putcha, B.-D.K. / Wright, E. / Brunzelle, J.S. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural basis for negative cooperativity within agonist-bound TR:RXR heterodimers. Authors: Putcha, B.D. / Wright, E. / Brunzelle, J.S. / Fernandez, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uvv.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uvv.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3uvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/3uvv ftp://data.pdbj.org/pub/pdb/validation_reports/uv/3uvv | HTTPS FTP |
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-Related structure data
Related structure data | 2h77S S: Starting model for refinement |
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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: 30090.807 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP Residues 147-407) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: THRA, NR1A1 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04625 |
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#2: Protein | Mass: 27346.766 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP Residues 225-462) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P19793 |
#3: Chemical | ChemComp-T3 / |
#4: Chemical | ChemComp-9CR / ( |
#5: 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: 4.03 Å3/Da / Density % sol: 69.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 100 mM HEPES (pH 7.3), 200 mM Tri-Sodium citrate dihydrate, 15% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.54984 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54984 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. all: 19341 / Num. obs: 19341 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.24 % / Biso Wilson estimate: 108.62 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.57 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.22 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H77 Resolution: 2.95→27.55 Å / Cor.coef. Fo:Fc: 0.9223 / Cor.coef. Fo:Fc free: 0.8882 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 114.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.686 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→27.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.11 Å / Total num. of bins used: 10
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