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Yorodumi- PDB-4k4j: Crystal structure of human Retinoid X Receptor alpha-ligand bindi... -
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-Basic information
Entry | Database: PDB / ID: 4k4j | ||||||
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Title | Crystal structure of human Retinoid X Receptor alpha-ligand binding domain complex with 9cUAB30 and the coactivator peptide GRIP-1 | ||||||
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Keywords | TRANSCRIPTION / ligand binding domain / cancer / 9-cis-UAB30 | ||||||
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 shuttle / TGFBR3 expression / retinoic acid 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 / Carnitine shuttle / TGFBR3 expression / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / DNA binding domain binding / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / 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 / SUMOylation of intracellular receptors / Heme signaling / 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 / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / 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 / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Xia, G. / Smith, C.D. / Muccio, D.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Defining the Communication between Agonist and Coactivator Binding in the Retinoid X Receptor alpha Ligand Binding Domain. Authors: Boerma, L.J. / Xia, G. / Qui, C. / Cox, B.D. / Chalmers, M.J. / Smith, C.D. / Lobo-Ruppert, S. / Griffin, P.R. / Muccio, D.D. / Renfrow, M.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k4j.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k4j.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k4j_validation.pdf.gz | 694.7 KB | Display | wwPDB validaton report |
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Full document | 4k4j_full_validation.pdf.gz | 699.7 KB | Display | |
Data in XML | 4k4j_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4k4j_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/4k4j ftp://data.pdbj.org/pub/pdb/validation_reports/k4/4k4j | HTTPS FTP |
-Related structure data
Related structure data | 4k6iC 3oapS S: Starting model for refinement C: citing same article (ref.) |
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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: 25897.021 Da / Num. of mol.: 1 / Fragment: ligand binding domain, UNP residues 228-458 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: P19793 / Gene: NR2B1, RXRA, RXRA NR2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793 |
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#2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 1 / Fragment: coactivator peptide, UNP residues 686-698 / Source method: obtained synthetically / Details: GRIP-1 from AnaSpec Inc / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596 |
#3: Chemical | ChemComp-1O8 / ( |
#4: 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: 2.21 Å3/Da / Density % sol: 44.23 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5-10% PEG4000, 2-5% Glycerol, 0.1M Bis-Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.315 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 2, 2004 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.315 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.53 Å / Num. all: 94263 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.45 % / Rmerge(I) obs: 0.048 / Rsym value: 0.322 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.47 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 1616 / Rsym value: 0.322 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OAP Resolution: 2→29.53 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→29.53 Å
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Refine LS restraints |
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