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Yorodumi- PDB-1ynw: Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid R... -
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-Basic information
Entry | Database: PDB / ID: 1ynw | ||||||
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Title | Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid Receptor DNA-Binding Domains Bound to a DR3 Response Element | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / VDR / RXR / Nuclear Receptor / Protein-DNA Complex / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / DNA binding domain binding / positive regulation of transporter activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / DNA binding domain binding / positive regulation of transporter activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / 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 / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / LBD domain binding / lithocholic acid binding / Carnitine metabolism / positive regulation of keratinocyte differentiation / retinoic acid binding / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / bile acid signaling pathway / intestinal absorption / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / mammary gland branching involved in pregnancy / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / decidualization / Synthesis of bile acids and bile salts / negative regulation of keratinocyte proliferation / 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 / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription coregulator binding / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / peptide binding / SUMOylation of intracellular receptors / skeletal system development / mRNA transcription by RNA polymerase II / 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 / cell morphogenesis / 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 / intracellular calcium ion homeostasis / calcium ion transport / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Shaffer, P.L. / Gewirth, D.T. | ||||||
Citation | Journal: J.Steroid Biochem.Mol.Biol. / Year: 2004 Title: Structural analysis of RXR-VDR interactions on DR3 DNA Authors: Shaffer, P.L. / Gewirth, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ynw.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ynw.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ynw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ynw_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 1ynw_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 1ynw_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1ynw_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1ynw ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1ynw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5564.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DR3 Response Element |
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#2: DNA chain | Mass: 5457.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DR3 Response Element |
#3: Protein | Mass: 12784.103 Da / Num. of mol.: 1 / Fragment: DNA-binding Domain (Residues 16-125) / Mutation: P61A,F62A,H75A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VDR, NR1I1 / Plasmid: pET11a-VDR(RPKLS) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11473 |
#4: Protein | Mass: 11642.225 Da / Num. of mol.: 1 / Fragment: DNA-binding Domain (Residues 130-228) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: pGEX-RXR(SANE) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19793 |
#5: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.3 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, ammonium citrate, Tris, glycerol, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1808 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1808 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 18127 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1844 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KB4 and 1DSZ Resolution: 3→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 800311.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.7974 Å2 / ksol: 0.287038 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
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Xplor file |
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