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Yorodumi- PDB-6jez: Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jez | ||||||
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Title | Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization | ||||||
Components |
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Keywords | HORMONE / turn-on fluorescent probe / TCC probe / covalent labeling / histidine | ||||||
Function / homology | Function and homology information enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / dense fibrillar component / SUMOylation of intracellular receptors / thyroid hormone mediated signaling pathway / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / core mediator complex / regulation of vitamin D receptor signaling pathway / positive regulation of parathyroid hormone secretion / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / vitamin D binding / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / negative regulation of ossification / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / embryonic hemopoiesis / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / megakaryocyte development / erythrocyte development / response to aldosterone / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / regulation of calcium ion transport / decidualization / general transcription initiation factor binding / negative regulation of neuron differentiation / positive regulation of transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / animal organ regeneration / heterochromatin / ubiquitin ligase complex / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / 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 / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / skeletal system development / nuclear estrogen receptor binding / promoter-specific chromatin binding / apoptotic signaling pathway / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / animal organ morphogenesis / brain development / euchromatin / Heme signaling / mRNA transcription by RNA polymerase II / cell morphogenesis / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / intracellular calcium ion homeostasis Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kojima, H. / Yamamoto, K. / Itoh, T. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2020 Title: Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins. Authors: Kojima, H. / Fujita, Y. / Takeuchi, R. / Ikebe, Y. / Ohashi, N. / Yamamoto, K. / Itoh, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jez.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jez.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6jez ftp://data.pdbj.org/pub/pdb/validation_reports/je/6jez | HTTPS FTP |
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-Related structure data
Related structure data | 6jeyC 6jf0C 2zlcS 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: 30595.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13053 |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648 |
#3: Chemical | ChemComp-YSV / ( |
#4: Chemical | ChemComp-EJO / |
#5: 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: 2.17 Å3/Da / Density % sol: 43.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MOPS-Na pH 7.0, 0.1 M sodium formate, 15% PEG4000, 5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41.75 Å / Num. obs: 12346 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.3→2.39 Å / Rmerge(I) obs: 0.109 / Num. unique obs: 1377 / CC1/2: 0.989 / Rpim(I) all: 0.066 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZLC Resolution: 2.3→29.18 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.874 / SU B: 16.123 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.255 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.774 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→29.18 Å
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