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- PDB-2o4j: Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain... -
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Basic information
Entry | Database: PDB / ID: 2o4j | ||||||
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Title | Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205 | ||||||
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![]() | HORMONE/GROWTH FACTOR RECEPTOR / Nuclear receptor-ligand complex / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | ![]() negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / SUMOylation of intracellular receptors / retinal pigment epithelium development / Nuclear Receptor transcription pathway / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / positive regulation of parathyroid hormone secretion / core mediator complex / regulation of vitamin D receptor signaling pathway / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / cellular response to vitamin D / vitamin D binding / calcitriol binding / lithocholic acid binding / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / phosphate ion transmembrane transport / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / intestinal absorption / positive regulation of vitamin D receptor signaling pathway / positive regulation of hepatocyte proliferation / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / negative regulation of ossification / nuclear thyroid hormone receptor binding / lens development in camera-type eye / embryonic hemopoiesis / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / response to aldosterone / RSV-host interactions / erythrocyte development / fat cell differentiation / mammary gland branching involved in pregnancy / regulation of calcium ion transport / nuclear steroid receptor activity / monocyte differentiation / decidualization / general transcription initiation factor binding / animal organ regeneration / negative regulation of neuron differentiation / negative regulation of keratinocyte proliferation / hematopoietic stem cell differentiation / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / nuclear retinoid X receptor binding / heterochromatin / retinoic acid receptor signaling pathway / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / intracellular receptor signaling pathway / lactation / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / T-tubule / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / cellular response to epidermal growth factor stimulus / positive regulation of erythrocyte differentiation / liver development / animal organ morphogenesis / nuclear estrogen receptor binding / nuclear receptor binding / skeletal system development / transcription coregulator activity / apoptotic signaling pathway / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / promoter-specific chromatin binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / euchromatin Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vanhooke, J.L. / Benning, M.M. / DeLuca, H.F. | ||||||
![]() | ![]() Title: New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations. Authors: Vanhooke, J.L. / Tadi, B.P. / Benning, M.M. / Plum, L.A. / Deluca, H.F. #1: ![]() Title: Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D3 Hormone Analogues and a LXXLL-Containing Coactivator Peptide Authors: Vanhooke, J.L. / Benning, M.M. / Bauer, C.B. / Pike, J.W. / DeLuca, H.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.6 KB | Display | ![]() |
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PDB format | ![]() | 51.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 762.6 KB | Display | ![]() |
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Full document | ![]() | 764.7 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2o4rC ![]() 1rjkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is composed of one molecule of VDR (chain A), one molecule of the synthetic peptide (chain C), and one ligand molecule (residue name VD4). The asymmetric unit contains one biological unit. |
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Components
#1: Protein | Mass: 32983.730 Da / Num. of mol.: 1 / Fragment: ligand binding domain Mutation: residues Ser165 through Pro211 are deleted from the protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP 205 NR2 Box Peptide / Source method: obtained synthetically / Details: synthesized at UW-Madison Biotechnology Center / References: UniProt: Q15648 |
#3: Chemical | ChemComp-VD4 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.03 % |
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Crystal grow | Temperature: 295 K / Method: macroseeding in batch / pH: 7 Details: PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER PROTEUM R / Detector: CCD / Date: Nov 30, 2005 / Details: Montel Optics |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→42.5 Å / Num. all: 27636 / Num. obs: 27577 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rsym value: 0.0448 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.74→1.85 Å / Redundancy: 3.54 % / Mean I/σ(I) obs: 2.86 / Num. unique all: 4160 / Rsym value: 0.321 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RJK Resolution: 1.74→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.362 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.128 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.413 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.786 Å / Total num. of bins used: 20
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