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Yorodumi- PDB-3kwy: Crystal structure of RXRalpha ligand binding domain in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 3kwy | ||||||
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Title | Crystal structure of RXRalpha ligand binding domain in complex with triphenyltin and a coactivator fragment | ||||||
Components |
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Keywords | TRANSCRIPTION / nuclear receptor transcription organotin / DNA-binding / Host-virus interaction / Isopeptide bond / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger / Activator / Phosphoprotein | ||||||
Function / homology | Function and homology information 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 receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex ...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 receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / 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 / response to retinoic acid / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / 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 / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / cell differentiation / receptor complex / nuclear body / protein dimerization activity / 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 / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | le Maire, A. / Bourguet, W. | ||||||
Citation | Journal: Cell.Mol.Life Sci. / Year: 2010 Title: A structural view of nuclear hormone receptor: endocrine disruptor interactions. Authors: le Maire, A. / Bourguet, W. / Balaguer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kwy.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kwy.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kwy_validation.pdf.gz | 798 KB | Display | wwPDB validaton report |
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Full document | 3kwy_full_validation.pdf.gz | 798.8 KB | Display | |
Data in XML | 3kwy_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3kwy_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/3kwy ftp://data.pdbj.org/pub/pdb/validation_reports/kw/3kwy | HTTPS FTP |
-Related structure data
Related structure data | 2p1tS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27269.514 Da / Num. of mol.: 1 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19793 |
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#2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 1 / Fragment: Nuclear Receptor box 2 (UNP residue 686-698) / Source method: obtained synthetically / References: UniProt: Q15596 |
#3: Chemical | ChemComp-T9T / |
#4: Chemical | ChemComp-ACT / |
#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: 2.06 Å3/Da / Density % sol: 40.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: PEG 4000, acetate ammonium, Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. all: 11258 / Num. obs: 11258 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Rsym value: 0.075 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.398 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P1T Resolution: 2.3→28.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.941 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.717 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→28.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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