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Yorodumi- PDB-1xvp: crystal structure of CAR/RXR heterodimer bound with SRC1 peptide,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xvp | ||||||
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Title | crystal structure of CAR/RXR heterodimer bound with SRC1 peptide, fatty acid and CITCO | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / CAR / RXR / CITCO / SRC1 | ||||||
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 / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / positive regulation of female receptivity / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / hypothalamus development / male mating behavior / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / 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 / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription coregulator binding / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / 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 / hippocampus development / nuclear estrogen receptor binding / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / cerebral cortex development / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / double-stranded DNA binding / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / cytoskeleton / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Xu, R.X. / Lambert, M.H. / Wisely, B.B. / Warren, E.N. / Weinert, E.E. / Waitt, G.M. / Williams, J.D. / Moore, L.B. / Willson, T.M. / Moore, J.T. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: A Structural Basis for Constitutive Activity in the Human CAR/RXRalpha Heterodimer. Authors: Xu, R.X. / Lambert, M.H. / Wisely, B.B. / Warren, E.N. / Weinert, E.E. / Waitt, G.M. / Williams, J.D. / Collins, J.L. / Moore, L.B. / Willson, T.M. / Moore, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xvp.cif.gz | 212.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xvp.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xvp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1xvp_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1xvp_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 1xvp_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/1xvp ftp://data.pdbj.org/pub/pdb/validation_reports/xv/1xvp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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5 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 26509.701 Da / Num. of mol.: 2 / Fragment: LBD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I3, CAR / Production host: Escherichia coli (E. coli) / References: UniProt: P19793 #2: Protein | Mass: 28278.959 Da / Num. of mol.: 2 / Fragment: LBD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14994 |
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-Protein/peptide , 1 types, 4 molecules EFGH
#3: Protein/peptide | Mass: 1633.916 Da / Num. of mol.: 4 / Fragment: Synthetic peptide-13 residues / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) Homo sapiens (human) / References: GenBank: 22538455, UniProt: Q15788*PLUS |
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-Non-polymers , 3 types, 101 molecules
#4: Chemical | #5: Chemical | ChemComp-CID / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Lisium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 62518 / Num. obs: 53979 / % possible obs: 86.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4525 / Rsym value: 0.418 / % possible all: 73.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: coordinates from twinned data restrained individual B-refinement with the twinning operator= -k,-h,-l twinning fraction= 0.401
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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