[English] 日本語
![](img/lk-miru.gif)
- PDB-3a2h: Crystal structure of the rat vitamin D receptor ligand binding do... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3a2h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205 | ||||||
![]() |
| ||||||
![]() | HORMONE RECEPTOR / TRANSCRIPTION / hormone/growth factor receptor / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Zinc-finger / Activator / Receptor | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kakuda, S. / Takimoto-Kamimura, M. | ||||||
![]() | ![]() Title: Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone Authors: Kakuda, S. / Ishizuka, S. / Eguchi, H. / Mizwicki, M.T. / Norman, A.W. / Takimoto-Kamimura, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 65.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 763 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 766.8 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a2iC ![]() 3a2jC ![]() 1rk3S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30055.498 Da / Num. of mol.: 1 / Fragment: ligand binding domain, residues 116-423 / Mutation: DEL(165-211) mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) ![]() |
#3: Chemical | ChemComp-TEJ / ( |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE LIGAND TEJ CAN BE CALLED AS TEI-9647. |
Sequence details | THIS PROTEIN VITAMIN D3 RECEPTOR IS A DELETION MUTANT. THE RESIDUES 165-211 WERE DELETED. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.15 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 9008 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.2 / Num. measured all: 28263 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.3 / % possible all: 96.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1rk3 Resolution: 2.5→40.36 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.854 / SU B: 11.654 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 1.311 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 27.112 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
|