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Yorodumi- PDB-4ite: Crystal structure of the human vitamin D receptor ligand binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ite | ||||||
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Title | Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(2H-tetrazol-2-yl)ethyl]vitamin D3 | ||||||
Components | Vitamin D3 receptor | ||||||
Keywords | TRANSCRIPTION / Hormone receptor | ||||||
Function / homology | Function and homology information regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / calcitriol binding / positive regulation of apoptotic process involved in mammary gland involution / vitamin D response element binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / calcitriol binding / positive regulation of apoptotic process involved in mammary gland involution / vitamin D response element binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / intracellular calcium ion homeostasis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / calcium ion transport / nuclear receptor activity / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Kakuda, S. / Takimoto-Kamimura, M. | ||||||
Citation | Journal: ACS MED.CHEM.LETT. / Year: 2013 Title: Synthesis of 2 alpha-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo Authors: Matsuo, M. / Hasegawa, A. / Takano, M. / Saito, H. / Kakuda, S. / Chida, T. / Takagi, K. / Ochiai, E. / Horie, K. / Harada, Y. / Takimoto-Kamimura, M. / Takenouchi, K. / Sawada, D. / Kittaka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ite.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ite.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 4ite.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/4ite ftp://data.pdbj.org/pub/pdb/validation_reports/it/4ite | HTTPS FTP |
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-Related structure data
Related structure data | 4itfC 1db1S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 29805.342 Da / Num. of mol.: 1 / Fragment: ligand binding domain, residues 118-427 / Mutation: DEL(165-215) mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VDR / Production host: Escherichia coli (E. coli) / References: UniProt: P11473 |
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#2: Chemical | ChemComp-TEY / ( |
#3: Water | ChemComp-HOH / |
Sequence details | THIS ENTRY IS DELETION MUTANT. RESIDUES 165-215 WERE DELETED. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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Detector | Detector: CCD / Date: Nov 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 11281 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.2 % |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 21.3 / Num. unique all: 11281 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DB1 Resolution: 2.49→37.03 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.335 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.096 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→37.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.491→2.556 Å / Total num. of bins used: 20
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