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- PDB-1zeo: Crystal Structure of Human PPAR-gamma Ligand Binding Domain Compl... -

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Basic information

Entry
Database: PDB / ID: 1zeo
TitleCrystal Structure of Human PPAR-gamma Ligand Binding Domain Complexed with an Alpha-Aryloxyphenylacetic Acid Agonist
ComponentsPeroxisome proliferator activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor / Ligand Binding Domain / LBD / Alpha helix sandwich / PPAR-RXR heterodimer
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding ...prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of blood vessel endothelial cell migration / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / cell fate commitment / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of MAPK cascade / retinoic acid receptor signaling pathway / cell maturation / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / response to nutrient / negative regulation of miRNA transcription / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / regulation of blood pressure / lipid metabolic process / positive regulation of miRNA transcription / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
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 / Double treble clef zinc finger, C4 type / 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
Chem-C01 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShi, G.Q. / Dropinski, J.F. / McKeever, B.M. / Adams, A.D. / MacNaul, K.L. / Elbrecht, A. / Berger, J.P. / Zhou, G. / Doebber, T.W.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Design and Synthesis of alpha-Aryloxyphenylacetic Acid Derivatives: A Novel Class of PPAR alpha/gamma Dual Agonists with Potent Antihyperglycemic and Lipid Modulating Activity
Authors: Shi, G.Q. / Dropinski, J.F. / McKeever, B.M. / Xu, S. / Becker, J.W. / Berger, J.P. / MacNaul, K.L. / Elbrecht, A. / Zhou, G. / Doebber, T.W. / Wang, P. / Chao, Y.-S. / Forrest, M. / Heck, J. ...Authors: Shi, G.Q. / Dropinski, J.F. / McKeever, B.M. / Xu, S. / Becker, J.W. / Berger, J.P. / MacNaul, K.L. / Elbrecht, A. / Zhou, G. / Doebber, T.W. / Wang, P. / Chao, Y.-S. / Forrest, M. / Heck, J.V. / Moller, D.E. / Jones, B.A.
History
DepositionApr 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999 SEQUENCE According to authors, residues Gly 201 and Ser 202 in Chains A and B are the remnants of ... SEQUENCE According to authors, residues Gly 201 and Ser 202 in Chains A and B are the remnants of a thrombin-cleavage site between Glutathione-S-transferase and PPARgamma-LBD
Remark 300BIOMOLECULE This entry contains the crystallographic asymmetric unit which consists of 2 chains, a ...BIOMOLECULE This entry contains the crystallographic asymmetric unit which consists of 2 chains, a PPARgamma homodimer, an artifact of crystallization. This could, however, serve as a model for how the biologically important heterodimer, PPAR-RXR could exist.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator activated receptor gamma
B: Peroxisome proliferator activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6123
Polymers63,1872
Non-polymers4251
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.573, 61.442, 118.051
Angle α, β, γ (deg.)90.00, 101.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome proliferator activated receptor gamma / PPAR-gamma


Mass: 31593.648 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain (LBD), residues 203-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-C01 / (2S)-(4-ISOPROPYLPHENYL)[(2-METHYL-3-OXO-5,7-DIPROPYL-2,3-DIHYDRO-1,2-BENZISOXAZOL-6-YL)OXY]ACETATE / ALPHA-ARYLOXYPHENYLACETIC ACID AGONIST


Mass: 424.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.95 M Trisodium Citrate, 0.1 M Tris/HCl, 1 mM TCEP, pH 8.5, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2003 / Details: Osmic "purple" confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→48.64 Å / Num. all: 22701 / Num. obs: 22701 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.13
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.18 / Num. unique all: 2341 / % possible all: 94.5

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Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNX2002phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SelenoMet PPARgamma-LBD complex

Resolution: 2.5→48.64 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 271300.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1020 4.8 %RANDOM
Rwork0.219 ---
all0.222 22674 --
obs0.222 21072 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2578 Å2 / ksol: 0.338155 e/Å3
Displacement parametersBiso mean: 57.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å29.2 Å2
2--8.74 Å20 Å2
3----8.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 31 114 4214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.403 74 4.4 %
Rwork0.351 1599 -
obs--74.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2C1.parC1.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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