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Yorodumi- PDB-3vtc: Crystal structure of rat vitamin D receptor bound to a partial ag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vtc | ||||||
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Title | Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3 | ||||||
Components |
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Keywords | HORMONE RECEPTOR / Transcription | ||||||
Function / homology | Function and homology information negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / dense fibrillar component / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / dense fibrillar component / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / vitamin D binding / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / response to aldosterone / mammary gland branching involved in pregnancy / regulation of calcium ion transport / decidualization / negative regulation of keratinocyte proliferation / heterochromatin / nuclear retinoid X receptor binding / T-tubule / lactation / skeletal system development / apoptotic signaling pathway / animal organ morphogenesis / euchromatin / mRNA transcription by RNA polymerase II / cell morphogenesis / intracellular calcium ion homeostasis / nuclear matrix / response to calcium ion / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / nuclear receptor activity / calcium ion transport / response to estradiol / heart development / sequence-specific DNA binding / cell differentiation / receptor complex / 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 / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Nakabayashi, M. / Kudo, T. / Tokiwa, H. / Makishima, M. / Yamada, S. / Ikura, T. / Ito, N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor. Authors: Kudo, T. / Ishizawa, M. / Maekawa, K. / Nakabayashi, M. / Watarai, Y. / Uchida, H. / Tokiwa, H. / Ikura, T. / Ito, N. / Makishima, M. / Yamada, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vtc.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vtc.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/3vtc ftp://data.pdbj.org/pub/pdb/validation_reports/vt/3vtc | HTTPS FTP |
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-Related structure data
Related structure data | 3vtbC 3vtdC 2zlcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 30595.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 116-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nr1i1, Vdr / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P13053 |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIS |
#3: Chemical | ChemComp-TK3 / ( |
#4: Chemical | ChemComp-EDO / |
#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: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS-Na, Na formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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Detector | Date: Dec 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 43106 / Biso Wilson estimate: 16.6 Å2 |
Reflection shell | Resolution: 1.5→1.55 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZLC Resolution: 1.5→27.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 221567.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.9161 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→27.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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