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- PDB-6l89: Human PPARgamma ligand binding domain complexed with Butyrolactone 1 -

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Basic information

Entry
Database: PDB / ID: 6l89
TitleHuman PPARgamma ligand binding domain complexed with Butyrolactone 1
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor Ligand binding domain Butyrolactone 1 Partial agonist
Function / homology
Function and homology information


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 / 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 / arachidonic acid binding ...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 / 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 / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding 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 / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / transcription coregulator binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / lipid metabolic process / regulation of circadian rhythm / PPARA activates gene expression / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / rhythmic process / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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 ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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
Similarity search - Domain/homology
Chem-E7C / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJang, D.M. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2011-0030001 Korea, Republic Of
CitationJournal: Biomolecules / Year: 2020
Title: Cyclin-Dependent Kinase 5 Inhibitor Butyrolactone I Elicits a Partial Agonist Activity of Peroxisome Proliferator-Activated Receptor gamma.
Authors: Ahn, S. / Jang, D.M. / Park, S.C. / An, S. / Shin, J. / Han, B.W. / Noh, M.
History
DepositionNov 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Peroxisome proliferator-activated receptor gamma
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2374
Polymers65,3882
Non-polymers8492
Water2,576143
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2374
Polymers65,3882
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area1760 Å2
ΔGint-12 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.623, 61.124, 119.762
Angle α, β, γ (deg.)90.000, 103.643, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 32693.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Chemical ChemComp-E7C / methyl (2R)-3-(4-hydroxyphenyl)-2-[[3-(3-methylbut-2-enyl)-4-oxidanyl-phenyl]methyl]-4-oxidanyl-5-oxidanylidene-furan-2-carboxylate / Butyrolactone I


Mass: 424.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38329 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 39.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.71 / Num. unique obs: 1920 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMH

3wmh


Resolution: 2.1→48.975 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.225 / SU B: 6.249 / SU ML: 0.162 / Average fsc free: 0.8805 / Average fsc work: 0.8964 / Cross valid method: FREE R-VALUE / ESU R: 0.27 / ESU R Free: 0.218
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2693 1734 5.042 %
Rwork0.2286 32656 -
all0.231 --
obs-34390 88.996 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.139 Å2
Baniso -1Baniso -2Baniso -3
1--0.132 Å20 Å2-0.108 Å2
2--0.412 Å2-0 Å2
3----0.204 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 62 148 4325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134265
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174140
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.6565753
X-RAY DIFFRACTIONr_angle_other_deg1.2031.5929629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94224.129201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54815820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2151516
X-RAY DIFFRACTIONr_chiral_restr0.0510.2558
X-RAY DIFFRACTIONr_chiral_restr_other0.0360.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
X-RAY DIFFRACTIONr_nbd_refined0.1990.2963
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23663
X-RAY DIFFRACTIONr_nbtor_refined0.1530.22125
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.220
X-RAY DIFFRACTIONr_nbd_other0.230.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.24
X-RAY DIFFRACTIONr_mcbond_it1.7373.3512058
X-RAY DIFFRACTIONr_mcbond_other1.7373.352057
X-RAY DIFFRACTIONr_mcangle_it3.0135.0012566
X-RAY DIFFRACTIONr_mcangle_other3.0135.0022567
X-RAY DIFFRACTIONr_scbond_it1.743.7482207
X-RAY DIFFRACTIONr_scbond_other1.743.7492208
X-RAY DIFFRACTIONr_scangle_it3.0045.53186
X-RAY DIFFRACTIONr_scangle_other3.0035.5013187
X-RAY DIFFRACTIONr_lrange_it5.87140.3044867
X-RAY DIFFRACTIONr_lrange_other5.86240.3024858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.314720.2811430X-RAY DIFFRACTION53.0555
2.154-2.2130.356960.291625X-RAY DIFFRACTION62.5363
2.213-2.2770.3291000.2891792X-RAY DIFFRACTION70.9677
2.277-2.3470.272980.2691983X-RAY DIFFRACTION78.4691
2.347-2.4240.3381050.2672150X-RAY DIFFRACTION89.9482
2.424-2.5090.3251060.2662292X-RAY DIFFRACTION98.1982
2.509-2.6030.3141120.2622243X-RAY DIFFRACTION99.8304
2.603-2.7090.2971110.2612181X-RAY DIFFRACTION99.8693
2.709-2.830.3051030.2492067X-RAY DIFFRACTION99.7243
2.83-2.9670.2941170.2561984X-RAY DIFFRACTION99.8574
2.967-3.1270.321220.2531895X-RAY DIFFRACTION99.6542
3.127-3.3160.274990.2241762X-RAY DIFFRACTION99.572
3.316-3.5440.294780.2181670X-RAY DIFFRACTION99.2054
3.544-3.8260.266890.2041571X-RAY DIFFRACTION99.3417
3.826-4.1890.239750.1821395X-RAY DIFFRACTION96.52
4.189-4.6790.164760.1741265X-RAY DIFFRACTION95.1739
4.679-5.3950.239590.1981111X-RAY DIFFRACTION97.1761
5.395-6.5890.204510.245999X-RAY DIFFRACTION99.7151
6.589-9.2380.182440.175784X-RAY DIFFRACTION98.9247
9.238-48.9750.244210.186454X-RAY DIFFRACTION97.137

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