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Yorodumi- PDB-1rkg: crystal structure of the rat vitamin D receptor ligand binding do... -
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-Basic information
Entry | Database: PDB / ID: 1rkg | ||||||
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Title | crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205 | ||||||
Components |
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Keywords | hormone/growth factor receptor / nuclear receptor-ligand complex / nuclear receptor-coactivator interactions / hormone-growth factor receptor COMPLEX | ||||||
Function / homology | Function and homology information 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 / positive regulation of parathyroid hormone secretion / regulation of vitamin D receptor signaling pathway / 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 / lithocholic acid binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / negative regulation of ossification / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / vitamin D receptor signaling pathway / peroxisome proliferator activated receptor binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / bile acid signaling pathway / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / histone acetyltransferase binding / cellular response to hepatocyte growth factor stimulus / response to aldosterone / RSV-host interactions / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / 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 / heterochromatin / erythrocyte development / 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 / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of erythrocyte differentiation / Activation of gene expression by SREBF (SREBP) / liver development / nuclear receptor coactivator activity / skeletal system development / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / apoptotic signaling pathway / animal organ morphogenesis / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / euchromatin / brain development / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / PPARA activates gene expression Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Vanhooke, J.L. / Benning, M.M. / Bauer, C.B. / Pike, J.W. / DeLuca, H.F. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D(3) 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rkg.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rkg.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/1rkg ftp://data.pdbj.org/pub/pdb/validation_reports/rk/1rkg | HTTPS FTP |
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-Related structure data
Related structure data | 1rjkSC 1rk3C 1rkhC 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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2 |
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Unit cell |
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Details | The asymmetric unit contains one biological unit. The biological unit is composed of one molecule of VDR, one ligand molecule (2MbisP), and one molecule of the synthetic peptide |
-Components
#1: Protein | Mass: 32983.730 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Mutation: Chain A, DEL(165-211) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: VDR, NR1I1 / Plasmid: pET-29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) CodonPlus RIL / References: UniProt: P13053 |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q15648 |
#3: Chemical | ChemComp-VD1 / |
#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: 2.05 Å3/Da / Density % sol: 39.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: BRUKER PROTEUM R / Detector: CCD / Date: Jan 2, 2003 |
Radiation | Monochromator: Montel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.4 Å / Num. all: 22362 / Num. obs: 22171 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rsym value: 0.032 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.9→1.99 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.153 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1RJK Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.198 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.948 Å / Total num. of bins used: 20
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