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- PDB-6l8b: The ligand-free structure of human PPARgamma LBD -

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Basic information

Entry
Database: PDB / ID: 6l8b
TitleThe ligand-free structure of human PPARgamma LBD
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor Ligand binding domain TRANSCRIPTION Ligand-free
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 / STAT family protein binding / WW domain 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 / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / white fat cell differentiation / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / 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 / negative regulation of signaling receptor activity / epithelial cell differentiation / 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 / positive regulation of apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / 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 / : / 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. ...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
Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 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


Theoretical massNumber of molelcules
Total (without water)64,5612
Polymers64,5612
Non-polymers00
Water2,864159
1
A: Peroxisome proliferator-activated receptor gamma

B: Peroxisome proliferator-activated receptor gamma


Theoretical massNumber of molelcules
Total (without water)64,5612
Polymers64,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2070 Å2
ΔGint-11 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.150, 62.256, 119.504
Angle α, β, γ (deg.)90.000, 102.508, 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: 32280.350 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.05 %
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: 11C / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 38322 / % possible obs: 98 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.625
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.583 / Num. unique obs: 1932

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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: 3VSO

3vso


Resolution: 2.102→29.345 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: FREE R-VALUE / ESU R: 0.25 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2675 1769 4.97 %
Rwork0.2181 --
all0.221 --
obs-35593 90.889 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.357 Å2-0 Å2-0.048 Å2
2--0.133 Å20 Å2
3----0.427 Å2
Refinement stepCycle: LAST / Resolution: 2.102→29.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 0 159 4367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134307
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174201
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.6365808
X-RAY DIFFRACTIONr_angle_other_deg2.2211.5769788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65124.098205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38315841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1371516
X-RAY DIFFRACTIONr_chiral_restr0.050.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024658
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02822
X-RAY DIFFRACTIONr_nbd_refined0.1920.2907
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.23386
X-RAY DIFFRACTIONr_nbtor_refined0.150.22117
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0560.21770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2171
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.225
X-RAY DIFFRACTIONr_nbd_other0.260.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.211
X-RAY DIFFRACTIONr_mcbond_it1.3523.0072105
X-RAY DIFFRACTIONr_mcbond_other1.3523.0062104
X-RAY DIFFRACTIONr_mcangle_it2.3394.4892625
X-RAY DIFFRACTIONr_mcangle_other2.3384.492626
X-RAY DIFFRACTIONr_scbond_it1.4433.2482202
X-RAY DIFFRACTIONr_scbond_other1.4433.2492203
X-RAY DIFFRACTIONr_scangle_it2.4454.7673178
X-RAY DIFFRACTIONr_scangle_other2.4444.7683179
X-RAY DIFFRACTIONr_lrange_it4.95335.2054823
X-RAY DIFFRACTIONr_lrange_other4.94535.2144809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.1560.286710.2841597X-RAY DIFFRACTION57.1037
2.156-2.2150.296890.271972X-RAY DIFFRACTION73.8181
2.215-2.2790.2771020.2562145X-RAY DIFFRACTION83.4385
2.279-2.3490.3011300.2372275X-RAY DIFFRACTION90.5838
2.349-2.4260.3131220.2392231X-RAY DIFFRACTION92.13
2.426-2.5110.2841300.2242221X-RAY DIFFRACTION94.3419
2.511-2.6050.2721310.2232197X-RAY DIFFRACTION97.2431
2.605-2.7110.297950.2342150X-RAY DIFFRACTION97.9921
2.711-2.8320.2741020.2262074X-RAY DIFFRACTION97.9298
2.832-2.9690.2691000.2312011X-RAY DIFFRACTION98.5068
2.969-3.1290.292940.2261871X-RAY DIFFRACTION97.181
3.129-3.3180.259930.2321743X-RAY DIFFRACTION96.4286
3.318-3.5460.261940.2121683X-RAY DIFFRACTION99.1076
3.546-3.8290.219910.1861571X-RAY DIFFRACTION99.4614
3.829-4.1920.25830.1871448X-RAY DIFFRACTION98.0782
4.192-4.6830.246580.1781310X-RAY DIFFRACTION96.6102
4.683-5.3990.223580.2061136X-RAY DIFFRACTION96.837
5.399-6.5930.299610.223993X-RAY DIFFRACTION99.6219
6.593-9.2440.265330.188779X-RAY DIFFRACTION95.4172
9.244-29.3450.276320.236417X-RAY DIFFRACTION91.2602

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