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- PDB-2o4r: Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o4r | ||||||
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Title | Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20E 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 | ![]() enucleate erythrocyte development / negative regulation of bone trabecula formation / positive regulation of type II interferon-mediated signaling pathway / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / SUMOylation of intracellular receptors ...enucleate erythrocyte development / negative regulation of bone trabecula formation / positive regulation of type II interferon-mediated signaling pathway / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / SUMOylation of intracellular receptors / G0 to G1 transition / thyroid hormone receptor signaling pathway / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / dense fibrillar component / core mediator complex / regulation of vitamin D receptor signaling pathway / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / vitamin D binding / calcitriol binding / vitamin D response element binding / lithocholic acid binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / nuclear retinoic acid receptor binding / mediator complex / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / negative regulation of ossification / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / intestinal absorption / bile acid signaling pathway / lens development in camera-type eye / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / nuclear thyroid hormone receptor binding / megakaryocyte development / histone acetyltransferase binding / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / response to aldosterone / RSV-host interactions / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / fat cell differentiation / mammary gland branching involved in pregnancy / regulation of calcium ion transport / monocyte differentiation / decidualization / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / heterochromatin / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / T-tubule / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / liver development / skeletal system development / promoter-specific chromatin binding / nuclear estrogen receptor binding / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / apoptotic signaling pathway / transcription coregulator activity / animal organ morphogenesis / Heme signaling / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / brain development 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 | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 740.7 KB | Display | ![]() |
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Full document | ![]() | 741.5 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2o4jC ![]() 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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Unit cell |
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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 VD5). 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-VD5 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.5 % |
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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: 1.98→42.5 Å / Num. all: 19228 / Num. obs: 19195 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.03 % / Rsym value: 0.0447 / Net I/σ(I): 22.77 |
Reflection shell | Resolution: 1.98→2.08 Å / Redundancy: 3.61 % / Mean I/σ(I) obs: 4.49 / Num. unique all: 2611 / Rsym value: 0.186 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1RJK Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.149 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.173 / 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: 26.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20
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