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- PDB-1prg: LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVA... -

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Basic information

Entry
Database: PDB / ID: 1prg
TitleLIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
ComponentsPROTEIN (PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA)
KeywordsGENE REGULATION / THIAZOLIDINEDIONE / LIGAND-BINDING DOMAIN / NUCLEAR RECEPTOR / APO / TRANSCRIPTION FACTOR / ORPHAN RECEPTOR
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity ...prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / 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 blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / epithelial cell differentiation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / transcription coregulator binding / fatty acid metabolic process / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / regulation of blood pressure / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsNolte, R.T. / Wisely, G.B. / Milburn, M.V.
CitationJournal: 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
DepositionJul 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA)
B: PROTEIN (PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA)


Theoretical massNumber of molelcules
Total (without water)61,6682
Polymers61,6682
Non-polymers00
Water10,178565
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.870, 62.000, 118.340
Angle α, β, γ (deg.)90.00, 102.66, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.112745, 0.983997, 0.137977), (0.978875, -0.133832, 0.15457), (0.170562, 0.117636, -0.9783))

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Components

#1: Protein PROTEIN (PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA) / E DOMAIN


Mass: 30833.850 Da / Num. of mol.: 2 / Fragment: LBD (LIGAND BINDING DOMAIN), RESIDUES 207-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEAR / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5
Details: VAPOR DIFFUSION METHOD, HANGING DROP TECHNIQUE, 1.4M SODIUM CITRATE, 100MM HEPES, PH 7.5
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1drop
35 mMdithiothreitol1drop
4100 mM1dropNaCl
52 mMEDTA1drop
61.4 Msodium citrate1drop
7100 mMHEPES1drop
81.4 Msodium citrate1reservoir
9100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. obs: 89611 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.264 / % possible all: 68
Reflection
*PLUS
Num. obs: 27817 / Num. measured all: 89611
Reflection shell
*PLUS
% possible obs: 68 %

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Processing

Software
NameVersionClassification
PHASESphasing
CCP4model building
CNS0. 0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→60 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 714023.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED DATA CUTOFF HIGH (ABS(F)) : 714023.09 DATA CUTOFF LOW ( ABS(F)) : 0.000000
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1122 4 %RANDOM
Rwork0.246 ---
obs0.246 27817 83.8 %-
Solvent computationSolvent model: SHRINK MASK | SHELL MODEL / Bsol: 120 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-1.61 Å2
2---12.46 Å20 Å2
3---13.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 0 565 4897
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 137 3.9 %
Rwork0.299 3391 -
obs--64.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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