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Yorodumi- PDB-2zxm: A New Class of Vitamin D Receptor Ligands that Induce Structural ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zxm | ||||||
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Title | A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket | ||||||
Components |
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Keywords | TRANSCRIPTION / Nuclear receptor-antagonist complex / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Receptor / Transcription regulation / Zinc / Zinc-finger / Activator | ||||||
Function / homology | Function and homology information negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / vitamin D binding / calcitriol binding / positive regulation of apoptotic process involved in mammary gland involution / vitamin D response element binding / lithocholic acid binding / mediator complex / 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 / transcription coregulator activity / animal organ morphogenesis / euchromatin / mRNA transcription by RNA polymerase II / cell morphogenesis / nuclear matrix / response to calcium ion / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / calcium ion transport / nuclear receptor activity / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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: 3.01 Å | ||||||
Authors | Nakabayashi, M. / Ikura, T. / Ito, N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor Authors: Inaba, Y. / Yoshimoto, N. / Sakamaki, Y. / Nakabayashi, M. / Ikura, T. / Tamamura, H. / Ito, N. / Shimizu, M. / Yamamoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zxm.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zxm.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zxm ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zxm | HTTPS FTP |
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-Related structure data
Related structure data | 2zxnC 1rk3S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30595.037 Da / Num. of mol.: 1 / Fragment: Ligand binding domain, UNP residues 116-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nr1i1, Vdr / Plasmid: PET-14B / 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 / Fragment: Drip 205 NR2 box peptide, UNP residues 624-636 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: A1L0Z0 |
#3: Chemical | ChemComp-JB1 / ( |
#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: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS-Na, Na-Formate, PEG4000, Ethyleneglycol, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 5664 / % possible obs: 99.1 % / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.392 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RK3 Resolution: 3.01→38.62 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 108868.49 / 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: 12.4203 Å2 / ksol: 0.317761 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.01→38.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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