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- PDB-4em9: Human PPAR gamma in complex with nonanoic acids -

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Basic information

Entry
Database: PDB / ID: 4em9
TitleHuman PPAR gamma in complex with nonanoic acids
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor / Retinoic acid receptor / Nucleus
Function / homology
Function and homology information


regulation of cholesterol transporter activity / low-density lipoprotein particle receptor biosynthetic process / prostaglandin receptor activity / negative regulation of pancreatic stellate cell proliferation / response to metformin / cellular response to vitamin E / macrophage derived foam cell differentiation / arachidonic acid binding / negative regulation of sequestering of triglyceride / negative regulation of receptor biosynthetic process ...regulation of cholesterol transporter activity / low-density lipoprotein particle receptor biosynthetic process / prostaglandin receptor activity / negative regulation of pancreatic stellate cell proliferation / response to metformin / cellular response to vitamin E / macrophage derived foam cell differentiation / arachidonic acid binding / negative regulation of sequestering of triglyceride / negative regulation of receptor biosynthetic process / negative regulation of vascular endothelial cell proliferation / cellular response to hyperoxia / lipoprotein transport / negative regulation of gene silencing by miRNA / positive regulation of fatty acid oxidation / positive regulation of vascular associated smooth muscle cell apoptotic process / pri-miRNA transcription by RNA polymerase II / white fat cell differentiation / DNA binding domain binding / negative regulation of collagen biosynthetic process / negative regulation of cholesterol storage / positive regulation of phagocytosis, engulfment / negative regulation of interferon-gamma-mediated signaling pathway / regulation of transcription involved in cell fate commitment / E-box binding / long-chain fatty acid transport / negative regulation of blood vessel endothelial cell migration / alpha-actinin binding / peroxisome proliferator activated receptor signaling pathway / LBD domain binding / cellular response to low-density lipoprotein particle stimulus / negative regulation of macrophage derived foam cell differentiation / cellular response to prostaglandin E stimulus / RNA polymerase II repressing transcription factor binding / positive regulation of oligodendrocyte differentiation / monocyte differentiation / response to lipid / response to vitamin A / negative regulation of vascular smooth muscle cell proliferation / positive regulation of fat cell differentiation / activating transcription factor binding / cell fate commitment / response to starvation / negative regulation of telomerase activity / fatty acid oxidation / hormone-mediated signaling pathway / lipid homeostasis / cell maturation / response to caffeine / fatty acid metabolic process / retinoid X receptor binding / negative regulation of acute inflammatory response / negative regulation of angiogenesis / positive regulation of DNA binding / response to immobilization stress / cellular response to retinoic acid / fatty acid binding / response to cold / negative regulation of smooth muscle cell proliferation / response to mechanical stimulus / epithelial cell differentiation / response to nutrient / peptide binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / animal organ regeneration / placenta development / regulation of circadian rhythm / lipid metabolic process / response to retinoic acid / estrogen receptor binding / steroid hormone receptor activity / RNA polymerase II transcription factor complex / regulation of blood pressure / protein self-association / nuclear receptor transcription coactivator activity / transcription regulatory region sequence-specific DNA binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of lipid metabolic process / rhythmic process / negative regulation of cell growth / cellular response to insulin stimulus / nuclear receptor activity / glucose homeostasis / RNA polymerase II regulatory region sequence-specific DNA binding / double-stranded DNA binding / drug binding / heart development / transcription regulatory region DNA binding / positive regulation of DNA-binding transcription factor activity / transcription initiation from RNA polymerase II promoter / signaling receptor activity / protein phosphatase binding / protein C-terminus binding / response to estrogen / cell differentiation / multicellular organism development / lipid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / intracellular membrane-bounded organelle
Nuclear hormone receptor / Zinc finger, nuclear hormone receptor-type / Nuclear hormone receptor, ligand-binding domain / Peroxisome proliferator-activated receptor / Peroxisome proliferator-activated receptor gamma / Zinc finger, NHR/GATA-type / Peroxisome proliferator-activated receptor gamma, N-terminal / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Retinoid X Receptor ...Nuclear hormone receptor / Zinc finger, nuclear hormone receptor-type / Nuclear hormone receptor, ligand-binding domain / Peroxisome proliferator-activated receptor / Peroxisome proliferator-activated receptor gamma / Zinc finger, NHR/GATA-type / Peroxisome proliferator-activated receptor gamma, N-terminal / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Retinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha
Peroxisome proliferator-activated receptor gamma
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiberato, M.V. / Nascimento, A.S. / Polikarpov, I.
CitationJournal: Plos One / Year: 2012
Title: Medium chain fatty acids are selective peroxisome proliferator activated receptor (PPAR) Gamma activators and pan-PPAR partial agonists
Authors: Liberato, M.V. / Nascimento, A.S. / Ayers, S.D. / Lin, J.Z. / Cvoro, A. / Silveira, R.L. / Martinez, L. / Souza, P.C. / Saidemberg, D. / Deng, T. / Amato, A.A. / Togashi, M. / Hsueh, W.A. / Phillips, K. / Palma, M.S. / Neves, F.A. / Skaf, M.S. / Webb, P. / Polikarpov, I.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release

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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)63,98010
Polymers62,8212
Non-polymers1,1598
Water5,603311
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9775
Polymers31,4101
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0035
Polymers31,4101
Non-polymers5934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Peroxisome proliferator-activated receptor gamma
hetero molecules

B: Peroxisome proliferator-activated receptor gamma
hetero molecules

A: Peroxisome proliferator-activated receptor gamma
hetero molecules

A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,96120
Polymers125,6424
Non-polymers2,31916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area7580 Å2
ΔGint-39 kcal/mol
Surface area44590 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)92.731, 62.255, 118.649
Angle α, β, γ (deg.)90.00, 101.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31410.488 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 235-505
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-KNA / nonanoic acid / Nonanoic acid


Mass: 158.238 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H18O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M tris-HCl, 0.9M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 2.1→32.8 Å / Num. all: 36878 / Num. obs: 36859 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.155 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEO
Resolution: 2.1→32.8 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1860 5.05 %RANDOM
Rwork0.2049 ---
Obs0.2065 36859 94.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.816 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3583 Å20 Å21.4107 Å2
2--2.2294 Å20 Å2
3----1.8711 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 78 311 4352
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0054135
f_angle_d0.7645569
f_dihedral_angle_d15.1991555
f_chiral_restr0.044644
f_plane_restr0.003704
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15550.3522940.2994173261
2.1555-2.21890.31141180.2649252989
2.2189-2.29050.29911570.2385266296
2.2905-2.37240.26241300.2322276197
2.3724-2.46730.2721270.2124277997
2.4673-2.57960.2821560.2112278498
2.5796-2.71550.23931370.2097278499
2.7155-2.88550.2771560.2146279699
2.8855-3.10820.22651550.21682872100
3.1082-3.42070.221390.20062824100
3.4207-3.91490.18771540.17442850100
3.9149-4.92970.18541730.1678281899
4.9297-32.80.24641640.208280896
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.90490.4198-0.23321.6142-0.00792.162-0.1813-0.1631-0.0690.08150.2108-0.173-0.1340.2534-0.03680.27390.1475-0.02110.31070.01540.210813.3685-0.531116.9623
22.39210.2-0.35451.0948-0.03192.6420.0281-0.196-0.00850.12310.01710.0823-0.11720.17-0.05050.32020.11270.02690.23970.02470.257730.0097-23.497933.7397
30.3292-0.21890.4390.3516-0.30630.7289-0.05250.0012-0.00240.00280.03010.0254-0.0480.01850.00860.31160.04580.02060.304-0.00390.293919.2558-12.748523.1014
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
11( CHAIN A AND ( RESID 207:477 OR RESID 501:503 ) )A207 - 477
21( CHAIN A AND ( RESID 207:477 OR RESID 501:503 ) )A501 - 503
32( CHAIN B AND ( RESID 207:474 OR RESID 501:502 ) )B207 - 474
42( CHAIN B AND ( RESID 207:474 OR RESID 501:502 ) )B501 - 502
53( CHAIN A AND RESID 601:771 ) OR ( CHAIN B AND RESID 601:740 )A601 - 771
63( CHAIN A AND RESID 601:771 ) OR ( CHAIN B AND RESID 601:740 )B601 - 740

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