[English] 日本語
![](img/lk-miru.gif)
- PDB-2prg: LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2prg | ||||||
---|---|---|---|---|---|---|---|
Title | LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA | ||||||
![]() |
| ||||||
![]() | COMPLEX (THIAZOLIDINEDIONE/RECEPTOR) / COMPLEX (THIAZOLIDINEDIONE-RECEPTOR) / LIGAND-BINDING DOMAIN / NUCLEAR RECEPTOR / APO / TRANSCRIPTION FACTOR / ORPHAN RECEPTOR / COMPLEX (THIAZOLIDINEDIONE-RECEPTOR) complex | ||||||
Function / homology | ![]() labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / positive regulation of female receptivity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / positive regulation of female receptivity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonate binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / STAT family protein binding / hypothalamus development / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of fatty acid metabolic process / male mating behavior / response to lipid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / negative regulation of BMP signaling pathway / estrous cycle / Synthesis of bile acids and bile salts / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / retinoic acid receptor signaling pathway / cell fate commitment / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / BMP signaling pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cell maturation / cellular response to hormone stimulus / negative regulation of signaling receptor activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / epithelial cell differentiation / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / cerebellum development / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / response to progesterone / nuclear receptor binding / hippocampus development / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nolte, R.T. / Wisely, G.B. / Milburn, M.V. | ||||||
![]() | ![]() Title: Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma. Authors: Nolte, R.T. / Wisely, G.B. / Westin, S. / Cobb, J.E. / Lambert, M.H. / Kurokawa, R. / Rosenfeld, M.G. / Willson, T.M. / Glass, C.K. / Milburn, M.V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 138.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1prgSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6963, -0.4441, 0.5639), Vector: |
-
Components
#1: Protein | Mass: 30997.021 Da / Num. of mol.: 2 / Fragment: LBD (LIGAND BINDING DOMAIN), RESIDUES 207-477 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 9396.225 Da / Num. of mol.: 1 / Fragment: FRAGMENT CONTAINING HD1 & HD2 RESIDUES 628-703 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH ROSIGLITAZONE (BRL-49653) REGISTRY # 122320-73-4 Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 26501 / % possible obs: 89.7 % / Observed criterion σ(I): -3 / Redundancy: 3.42 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.185 / % possible all: 58.3 |
Reflection shell | *PLUS % possible obs: 58.3 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PRG Resolution: 2.3→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 266280597.97 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: SHRINK MASK | SHELL MODEL / Bsol: 120 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|