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- PDB-6an1: Crystal structure of the complex between PPARgamma LBD and the li... -

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Basic information

Entry
Database: PDB / ID: 6an1
TitleCrystal structure of the complex between PPARgamma LBD and the ligand AM-879
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsNUCLEAR PROTEIN / Nuclear receptor / ligand binding domain
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 / STAT family protein binding / positive regulation of fatty acid metabolic process / 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 / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / 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 / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / negative regulation of MAPK cascade / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of miRNA transcription / peptide binding / 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 / positive regulation of miRNA transcription / regulation of blood pressure / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / 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 / DNA-binding transcription factor binding / cellular response to hypoxia / 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 / innate immune response / negative regulation of gene expression / 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-BKY / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.687 Å
AuthorsVeras, H. / Figueira, A.C. / le Maire, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/22246-0 Brazil
CitationJournal: Front Endocrinol (Lausanne) / Year: 2018
Title: Screening for PPAR Non-Agonist Ligands Followed by Characterization of a Hit, AM-879, with Additional No-Adipogenic and cdk5-Mediated Phosphorylation Inhibition Properties.
Authors: Ribeiro Filho, H.V. / Bernardi Videira, N. / Bridi, A.V. / Tittanegro, T.H. / Helena Batista, F.A. / de Carvalho Pereira, J.G. / de Oliveira, P.S.L. / Bajgelman, M.C. / Le Maire, A. / Figueira, A.C.M.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)65,6303
Polymers65,2452
Non-polymers3841
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-1 kcal/mol
Surface area24920 Å2
Unit cell
Length a, b, c (Å)93.321, 61.366, 118.450
Angle α, β, γ (deg.)90.00, 102.65, 90.00
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: 32622.746 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-BKY / 4-({2-[(1,3-dioxo-1,3-dihydro-2H-inden-2-ylidene)methyl]phenoxy}methyl)benzoic acid


Mass: 384.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H16O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.9M tri-sodium citrate, 100mM Hepes, 3.5% 1,2-propanediol, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45862 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45862 Å / Relative weight: 1
ReflectionResolution: 2.69→40.74 Å / Num. obs: 18387 / % possible obs: 99.58 % / Redundancy: 6.54 % / Net I/σ(I): 20.59

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.687→40.744 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 946 5.16 %
Rwork0.2181 --
obs0.2211 18347 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.687→40.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 29 12 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044203
X-RAY DIFFRACTIONf_angle_d0.7515679
X-RAY DIFFRACTIONf_dihedral_angle_d5.563084
X-RAY DIFFRACTIONf_chiral_restr0.043657
X-RAY DIFFRACTIONf_plane_restr0.005781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6873-2.8290.31291390.29092442X-RAY DIFFRACTION99
2.829-3.00620.31661420.27212447X-RAY DIFFRACTION100
3.0062-3.23820.33741380.26762495X-RAY DIFFRACTION100
3.2382-3.56390.28261450.24962472X-RAY DIFFRACTION100
3.5639-4.07920.32321250.21282506X-RAY DIFFRACTION100
4.0792-5.13770.25141420.19552506X-RAY DIFFRACTION100
5.1377-40.74880.23391150.19422533X-RAY DIFFRACTION98
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)
14.33094.604-1.77658.3519-2.11738.18750.3977-0.21570.02250.27780.071-0.3688-1.60070.4712-0.55580.59840.08770.09090.72890.01260.613827.5249-1.684930.0773
23.9102-4.1072-2.60837.22353.87084.35410.2595-0.65820.278-1.1074-0.3956-1.4718-0.55040.5565-0.15641.5416-0.06630.16181.19940.18931.193651.0819-4.632431.451
34.95273.12740.15437.3232-2.63886.2987-0.2408-0.7467-0.4604-0.2914-0.15130.19420.8526-0.97210.42030.64570.09510.08291.18840.15610.6211-4.42120.368320.3519
44.2570.71.52652.4346-0.98575.8065-0.48260.18970.1693-0.06090.36120.1472-0.70770.30720.01450.5482-0.01950.02630.87940.00230.43448.412213.1966-0.4526
55.60643.235-5.31684.587-3.18935.0965-0.270.61731.2032-0.48820.5630.2415-0.4378-0.7965-0.37130.68090-0.13490.87820.10040.707714.450523.030811.7639
62.05130.694-1.90571.4080.72468.4239-0.2205-0.51380.54360.30070.0992-0.3098-0.09261.09370.14570.61410.2151-0.05520.94490.05040.51899.411.302526.9108
74.79670.31930.21346.9333-3.78063.3816-0.5276-0.21890.3030.41580.076-1.0495-0.51530.80620.45470.6776-0.021-0.031.0299-0.0850.584422.373216.3686.1558
82.94890.25420.25852.49880.85735.1557-0.2653-0.7639-0.12160.20910.261-0.37010.26790.59710.05550.44760.1739-0.01650.73180.03730.460413.00214.047520.1531
91.82131.94461.02538.70476.46948.47250.2023-0.8581-0.73211.20940.7924-0.59882.27940.2014-0.61940.65170.18350.00180.85030.1420.57374.7215-5.451323.2657
105.41095.502-0.32535.5843-0.36490.29320.0359-0.9241-0.3986-0.1616-0.3449-1.29970.10250.4540.51180.7260.26870.00020.93060.02180.792222.83888.007921.4782
115.8685.8923-5.98975.9503-5.86376.78060.6761-3.20790.14572.0929-1.7045-0.9654-3.2972.20020.11581.5254-0.20350.08611.71250.03621.127621.697724.760925.0178
122.08120.61173.4277.87360.36056.72530.19130.4591-0.8497-0.1736-0.52050.59951.6054-0.49910.04830.8509-0.07360.02980.77640.02370.745921.2546-26.310927.8354
134.13441.7813.32845.57370.32472.99061.1642-1.6883-0.68420.9376-0.4332-0.05890.61350.3092-0.80.88280.16270.08581.32470.0540.60830.143-16.496949.0274
146.48762.3978-5.33842.7799-2.8324.80660.5028-2.0658-0.5515-0.395-1.1901-1.0347-0.04232.31281.23821.32390.0761-0.14451.65890.04880.868645.9411-9.673150.8565
154.07390.4157-0.2021.22541.18255.43980.0245-0.48650.06810.17570.1776-0.1836-0.31170.638-0.13780.65710.10420.0690.72930.07770.460133.6239-9.207535.5248
165.09820.3660.51034.7402-3.02645.67050.2939-0.0718-0.21890.08930.08250.6992-0.1952-0.7596-0.49560.40190.1371-0.04950.4512-0.01360.531419.1441-15.15224.1351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 431 through 457 )
2X-RAY DIFFRACTION2chain 'B' and (resid 458 through 474 )
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 251 )
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 333 )
7X-RAY DIFFRACTION7chain 'A' and (resid 334 through 364 )
8X-RAY DIFFRACTION8chain 'A' and (resid 365 through 403 )
9X-RAY DIFFRACTION9chain 'A' and (resid 404 through 430 )
10X-RAY DIFFRACTION10chain 'A' and (resid 431 through 459 )
11X-RAY DIFFRACTION11chain 'A' and (resid 460 through 475 )
12X-RAY DIFFRACTION12chain 'B' and (resid 208 through 225 )
13X-RAY DIFFRACTION13chain 'B' and (resid 226 through 251 )
14X-RAY DIFFRACTION14chain 'B' and (resid 252 through 276 )
15X-RAY DIFFRACTION15chain 'B' and (resid 277 through 377 )
16X-RAY DIFFRACTION16chain 'B' and (resid 378 through 430 )

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