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Yorodumi- PDB-2prg: LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2prg | ||||||
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Title | LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA | ||||||
Components |
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Keywords | COMPLEX (THIAZOLIDINEDIONE/RECEPTOR) / COMPLEX (THIAZOLIDINEDIONE-RECEPTOR) / LIGAND-BINDING DOMAIN / NUCLEAR RECEPTOR / APO / TRANSCRIPTION FACTOR / ORPHAN RECEPTOR / COMPLEX (THIAZOLIDINEDIONE-RECEPTOR) complex | ||||||
Function / homology | Function and homology information labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Complex I biogenesis / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Respiratory electron transport / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / response to retinoic acid / mitochondrial ATP synthesis coupled electron transport / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / mitochondrial respiratory chain complex I assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / NADH dehydrogenase (ubiquinone) activity / hippocampus development / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitochondrial membrane / aerobic respiration / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / cerebral cortex development / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / protein dimerization activity / mitochondrial inner membrane / positive regulation of apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nolte, R.T. / Wisely, G.B. / Milburn, M.V. | ||||||
Citation | Journal: Nature / Year: 1998 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2prg.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2prg.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 2prg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2prg_validation.pdf.gz | 518 KB | Display | wwPDB validaton report |
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Full document | 2prg_full_validation.pdf.gz | 540.3 KB | Display | |
Data in XML | 2prg_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 2prg_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/2prg ftp://data.pdbj.org/pub/pdb/validation_reports/pr/2prg | HTTPS FTP |
-Related structure data
Related structure data | 1prgSC 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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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.) Homo sapiens (human) / Cellular location: NUCLEUS / Gene: HUMAN PPAR GAMMA CDNA / Plasmid: PRSET A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): HPPARGAMMA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P37231 #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.) Homo sapiens (human) / Cellular location: NUCLEUS / Gene: SRC-1 CDNA / Plasmid: PRSET A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O43792, UniProt: Q15788*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Solvent computation | Solvent model: SHRINK MASK | SHELL MODEL / Bsol: 120 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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