+Open data
-Basic information
Entry | Database: PDB / ID: 4zsh | ||||||
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Title | RXR LBD in complex with 9-cis-13,14-dihydroretinoic acid | ||||||
Components |
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Keywords | TRANSCRIPTION / nuclear receptor / RXR | ||||||
Function / homology | Function and homology information DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism ...DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / locomotor rhythm / aryl hydrocarbon receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / 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 adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated 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 / regulation of cellular response to insulin stimulus / response to retinoic acid / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription coregulator binding / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / HATs acetylate histones / transcription regulator complex / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of DNA-templated transcription / chromatin / 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: 1.8 Å | ||||||
Authors | Rochel, N. / Krezel, W. / Ruhl, R. | ||||||
Citation | Journal: Plos Genet. / Year: 2015 Title: 9-cis-13,14-Dihydroretinoic Acid Is an Endogenous Retinoid Acting as RXR Ligand in Mice. Authors: Ruhl, R. / Krzyzosiak, A. / Niewiadomska-Cimicka, A. / Rochel, N. / Szeles, L. / Vaz, B. / Wietrzych-Schindler, M. / Alvarez, S. / Szklenar, M. / Nagy, L. / de Lera, A.R. / Krezel, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zsh.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zsh.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zsh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/4zsh ftp://data.pdbj.org/pub/pdb/validation_reports/zs/4zsh | HTTPS FTP |
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-Related structure data
Related structure data | 2zxzS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26856.039 Da / Num. of mol.: 1 / Fragment: residues 223 - 462 Source method: isolated from a genetically manipulated source Details: Ligand binding domain / Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pET15b Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Variant (production host): pLysS AG / References: UniProt: P19793 |
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#2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 1 / Fragment: residues 471 - 483 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS |
#3: Chemical | ChemComp-4XW / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.06 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: PEG3350 18%, calcium acetate 50 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 27 February 2013 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 22407 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rsym value: 0.05 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rsym value: 0.481 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZXZ Resolution: 1.8→25 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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