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Yorodumi- PDB-3a3z: Crystal structure of the human VDR ligand binding domain bound to... -
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-Basic information
Entry | Database: PDB / ID: 3a3z | ||||||
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Title | Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277A(C23S) | ||||||
Components | Vitamin D3 receptor | ||||||
Keywords | GENE REGULATION / Transcription / Structural Genomics / SPINE2 / Structural Proteomics in Europe 2 / SPINE-2 | ||||||
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 / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / 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 / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / 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 / intestinal absorption / bile acid signaling pathway / 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 / positive regulation of gene expression / chromatin / 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: 1.72 Å | ||||||
Authors | Sato, Y. / Antony, P. / Huet, T. / Sigueiro, R. / Rochel, N. / Moras, D. / Structural Proteomics in Europe 2 (SPINE-2) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Structure-function relationships and crystal structures of the vitamin D receptor bound 2 alpha-methyl-(20S,23S)- and 2 alpha-methyl-(20S,23R)-epoxymethano-1 alpha,25-dihydroxyvitamin D3 Authors: Antony, P. / Sigueiro, R. / Huet, T. / Sato, Y. / Ramalanjaona, N. / Rodrigues, L.C. / Mourino, A. / Moras, D. / Rochel, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a3z.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a3z.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 3a3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a3z_validation.pdf.gz | 766.4 KB | Display | wwPDB validaton report |
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Full document | 3a3z_full_validation.pdf.gz | 767.2 KB | Display | |
Data in XML | 3a3z_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3a3z_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/3a3z ftp://data.pdbj.org/pub/pdb/validation_reports/a3/3a3z | HTTPS FTP |
-Related structure data
Related structure data | 3a40C 1db1S 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
#1: Protein | Mass: 29805.342 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain, UNP residues 118-427 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P11473 | ||
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#2: Chemical | ChemComp-2MV / ( | ||
#3: Chemical | #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: 2.61 Å3/Da / Density % sol: 52.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10mM Tris, 100mM NaCl, 1nM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2009 |
Radiation | Monochromator: horizontally diffracting monochromator, Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 33546 / Num. obs: 32842 / % possible obs: 97.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.337 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DB1 Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.917 / SU ML: 0.064 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / 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: 12.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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