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- PDB-6qj5: X-ray structure of PPARgamma LBD with the ligand NV1380 -

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Basic information

Entry
Database: PDB / ID: 6qj5
TitleX-ray structure of PPARgamma LBD with the ligand NV1380
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsDNA BINDING PROTEIN / BUNDLE OF ALPHA-HELICES and SMALL FOUR-STRANDED BETA-SHEET / transcription factor / dna-binding / diabetes type II
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 / WW 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 / 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 / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / 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 / epithelial cell differentiation / negative regulation of signaling receptor activity / 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 / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / regulation of blood pressure / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / 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-H8R / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPochetti, G. / Montanari, R. / Capelli, D.
CitationJournal: J.Med.Chem. / Year: 2020
Title: A Novel N-Substituted Valine Derivative with Unique Peroxisome Proliferator-Activated Receptor gamma Binding Properties and Biological Activities.
Authors: Peiretti, F. / Montanari, R. / Capelli, D. / Bonardo, B. / Colson, C. / Amri, E.Z. / Grimaldi, M. / Balaguer, P. / Ito, K. / Roeder, R.G. / Pochetti, G. / Brunel, J.M.
History
DepositionJan 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)69,5153
Polymers69,1662
Non-polymers3491
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-3 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.600, 61.940, 119.400
Angle α, β, γ (deg.)90.000, 103.000, 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: 34582.906 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-H8R / (2~{S})-3-methyl-2-[(4-octoxyphenyl)carbonylamino]butanoic acid


Mass: 349.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.8M NaCitrate, 0.15M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2→58.17 Å / Num. obs: 43750 / % possible obs: 97 % / Redundancy: 3.1 % / Biso Wilson estimate: 52.64 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.052 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3104 / CC1/2: 0.48 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D6D

3d6d


Resolution: 2→51.24 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 34.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 2185 5.01 %
Rwork0.2313 41468 -
obs0.2337 43653 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.45 Å2 / Biso mean: 56.4269 Å2 / Biso min: 32.57 Å2
Refinement stepCycle: final / Resolution: 2→51.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 33 144 4163
Biso mean--63.46 54.8 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084387
X-RAY DIFFRACTIONf_angle_d1.075908
X-RAY DIFFRACTIONf_chiral_restr0.055682
X-RAY DIFFRACTIONf_plane_restr0.008748
X-RAY DIFFRACTIONf_dihedral_angle_d5.8712725
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.04310.47781050.4511244793
2.0431-2.09060.47581360.4147249193
2.0906-2.14290.40351400.3665264898
2.1429-2.20080.3891320.32258798
2.2008-2.26560.34821220.2922262897
2.2656-2.33870.27651510.2611261397
2.3387-2.42230.33741240.2462258697
2.4223-2.51930.30441310.236248993
2.5193-2.63390.25381310.2419262598
2.6339-2.77280.30061470.2294262398
2.7728-2.94650.2851550.2256262198
2.9465-3.1740.35131470.2565256797
3.174-3.49330.29151290.2187261296
3.4933-3.99860.2471380.212266999
3.9986-5.03720.25171400.1867255194
5.0372-51.240.22431570.2185271198

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