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- PDB-6d3e: PPARg LBD in Complex with SR1988 -

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Basic information

Entry
Database: PDB / ID: 6d3e
TitlePPARg LBD in Complex with SR1988
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / type 2 diabetes / nuclear receptor / drug discovery
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 / : / 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
Chem-FT7 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.395 Å
AuthorsFrkic, R.L. / Bruning, J.B.
CitationJournal: Nucl Receptor Res / Year: 2018
Title: Structural and Dynamic Elucidation of a Non-acid PPARgammaPartial Agonist: SR1988.
Authors: Frkic, R.L. / Chua, B.S. / Shin, Y. / Pascal, B.D. / Novick, S.J. / Kamenecka, T.M. / Griffin, P.R. / Bruning, J.B.
History
DepositionApr 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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)64,5853
Polymers64,1522
Non-polymers4331
Water3,189177
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

B: Peroxisome proliferator-activated receptor gamma


Theoretical massNumber of molelcules
Total (without water)64,5853
Polymers64,1522
Non-polymers4331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2080 Å2
ΔGint-11 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.040, 62.510, 118.650
Angle α, β, γ (deg.)90.000, 102.320, 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: 32076.189 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-FT7 / 1-[(2,4-difluorophenyl)methyl]-2,3-dimethyl-N-[(1R)-1-phenylpropyl]-1H-indole-5-carboxamide


Mass: 432.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26F2N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1.2M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.395→57.96 Å / Num. obs: 26013 / % possible obs: 98.3 % / Redundancy: 6 % / Biso Wilson estimate: 43.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.054 / Rrim(I) all: 0.136 / Net I/σ(I): 11.8
Reflection shellResolution: 2.395→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.276 / Num. measured all: 13591 / Num. unique obs: 2563 / CC1/2: 0.601 / Rpim(I) all: 0.575 / Rrim(I) all: 1.404 / Net I/σ(I) obs: 1.8 / % possible all: 93

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.11_2567refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R06

4r06


Resolution: 2.395→39.542 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.67
RfactorNum. reflection% reflection
Rfree0.2637 1285 4.95 %
Rwork0.2056 --
obs0.2084 25950 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 226.65 Å2 / Biso mean: 63.6991 Å2 / Biso min: 28.25 Å2
Refinement stepCycle: final / Resolution: 2.395→39.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 32 178 4406
Biso mean--105.52 59.39 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024315
X-RAY DIFFRACTIONf_angle_d0.425816
X-RAY DIFFRACTIONf_chiral_restr0.035675
X-RAY DIFFRACTIONf_plane_restr0.004732
X-RAY DIFFRACTIONf_dihedral_angle_d12.8252652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.395-2.49090.32461480.28372551269993
2.4909-2.60420.32731480.27392646279496
2.6042-2.74150.34521410.25562700284197
2.7415-2.91320.26171190.2352776289599
2.9132-3.1380.31061490.23962755290499
3.138-3.45370.26221500.215227702920100
3.4537-3.9530.27471460.191427802926100
3.953-4.97890.19321400.17428102950100
4.9789-39.54780.26091440.184628773021100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1414-0.7647-0.45481.5481-0.21024.4469-0.0983-0.0609-0.17540.04050.13950.2904-0.0458-0.4682-0.05020.27170.03310.03540.39750.05230.3829-0.399115.205614.9591
22.66130.1001-0.38780.31870.3053.4447-0.33370.35440.0865-0.33460.1471-0.2102-0.4560.16890.05920.5802-0.0190.01520.414-0.00010.448313.845233.25317.6498
31.62830.5517-0.11571.7552-0.1933.0757-0.1816-0.1781-0.1970.04830.08-0.17210.1020.4490.11930.3450.1610.0260.40680.00850.383412.691518.251618.943
42.6921.9657-0.16533.1716-0.50121.23180.193-0.5236-0.15480.3178-0.0756-0.9569-0.04060.644-0.10080.54760.14080.00190.6392-0.03180.495422.201525.686823.1838
52.57650.46832.30576.8872-0.27725.90170.35630.3814-0.9555-0.5197-0.140.21511.0879-0.1329-0.24240.77470.06050.08760.38010.00460.527219.7682-15.373826.5918
65.3267-0.33182.95053.05532.5224.29910.3798-1.1067-0.35880.5067-0.1099-0.2720.19960.1522-0.16810.8920.05770.06010.82780.11560.395337.7884-2.985849.6851
72.33610.1293-0.03321.98460.08194.00090.0088-0.1762-0.03950.26010.06980.1297-0.25130.1273-0.05130.46110.14590.06420.34680.02980.389828.703-0.314531.7015
86.41961.83692.03325.5073-0.0894.83350.17710.40010.78350.2344-0.01250.0531-0.80020.5233-0.15850.52870.05080.06370.48070.05360.459126.15719.110829.6787
90.4763-0.1471-0.43785.8903-0.33220.46720.1089-1.02910.7056-0.3438-0.05860.528-0.92080.2262-0.15971.17430.00420.22080.9166-0.1160.943449.67357.385931.4705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 204 through 237 )A204 - 237
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 302 )A238 - 302
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 430 )A303 - 430
4X-RAY DIFFRACTION4chain 'A' and (resid 431 through 476 )A431 - 476
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 225 )B206 - 225
6X-RAY DIFFRACTION6chain 'B' and (resid 226 through 276 )B226 - 276
7X-RAY DIFFRACTION7chain 'B' and (resid 277 through 430 )B277 - 430
8X-RAY DIFFRACTION8chain 'B' and (resid 431 through 455 )B431 - 455
9X-RAY DIFFRACTION9chain 'B' and (resid 456 through 476 )B456 - 476

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