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- PDB-8bff: Human PPARgamma in complex with MINCH bound to the AF-2 sub-pocket -

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Basic information

Entry
Database: PDB / ID: 8bff
TitleHuman PPARgamma in complex with MINCH bound to the AF-2 sub-pocket
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsNUCLEAR PROTEIN / PPAR gamma activation / MINCH / ligand binding domain / environmental contaminant
Function / homology
Function and homology information


prostaglandin receptor activity / regulation of cholesterol transporter 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 / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding ...prostaglandin receptor activity / regulation of cholesterol transporter 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 / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / 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 / 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 macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / 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 / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / peptide binding / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding
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. / c4 zinc finger in nuclear hormone receptors ...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
Chem-QG6 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUseini, A. / Straeter, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1052-Z6 Germany
CitationJournal: Environ Int / Year: 2023
Title: Structural basis of the activation of PPAR gamma by the plasticizer metabolites MEHP and MINCH.
Authors: Useini, A. / Engelberger, F. / Kunze, G. / Strater, N.
History
DepositionOct 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 2.0May 24, 2023Group: Non-polymer description / Refinement description / Category: chem_comp / struct_ncs_dom_lim
Item: _chem_comp.formula / _struct_ncs_dom_lim.beg_label_asym_id ..._chem_comp.formula / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5224
Polymers97,2383
Non-polymers2841
Water21612
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6972
Polymers32,4131
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma


Theoretical massNumber of molelcules
Total (without water)32,4131
Polymers32,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peroxisome proliferator-activated receptor gamma


Theoretical massNumber of molelcules
Total (without water)32,4131
Polymers32,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.181, 92.181, 89.509
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 207 and (name N or name...
d_2ens_1(chain "B" and ((resid 207 and (name N or name...
d_3ens_1(chain "C" and ((resid 207 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUTHRTHRAA207 - 29713 - 103
d_12TYRTYRLEULEUAA299 - 476105 - 282
d_21GLUGLUTHRTHRBB207 - 29713 - 103
d_22TYRTYRLEULEUBB299 - 476105 - 282
d_31GLUGLUTHRTHRCC207 - 29713 - 103
d_32TYRTYRLEULEUCC299 - 476105 - 282

NCS oper:
IDCodeMatrixVector
1given(-0.493074507624, -0.869986091381, -0.00131557369934), (-0.869987003996, 0.493073240504, 0.00117999015851), (-0.000377900838815, 0.00172635508764, -0.999998438443)46.1618788178, 26.6666192504, -46.1303184458
2given(0.638125321137, 0.769044866942, -0.0369603456998), (-0.765264669853, 0.628247335485, -0.140268565728), (-0.0846525817618, 0.1177933703, 0.989423398912)-3.01270495606, 51.6542673184, -11.521906237

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Components

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


Mass: 32412.576 Da / Num. of mol.: 3
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-QG6 / (1~{S},2~{R})-2-[(4~{R})-4-methylheptoxy]carbonylcyclohexane-1-carboxylic acid / MINCH


Mass: 284.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H28O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.5 30% PEG 2000 0.2 M Lithium sulfate 0.01 M guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→89.51 Å / Num. obs: 26138 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.191 / Net I/σ(I): 8.8
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 8.3 % / Rmerge(I) obs: 7.145 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1318 / CC1/2: 0.357 / Rpim(I) all: 2.607 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
DIALSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ATH, 3B1M, 6DHA

2ath

3b1m

6dha


Resolution: 2.6→79.83 Å / Cross valid method: FREE R-VALUE / σ(F): 204.38 / Phase error: 56.2441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2946 1745 7.08 %
Rwork0.266 22889 -
obs0.2975 24634 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→79.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 20 12 6116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00546223
X-RAY DIFFRACTIONf_angle_d0.7778389
X-RAY DIFFRACTIONf_chiral_restr0.0379980
X-RAY DIFFRACTIONf_plane_restr0.00381064
X-RAY DIFFRACTIONf_dihedral_angle_d13.10562376
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.19031816252
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.37705336686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.4037680.4248782X-RAY DIFFRACTION35.27
2.68-2.760.3891430.35971935X-RAY DIFFRACTION89.21
2.76-2.860.38971510.34392009X-RAY DIFFRACTION91.86
2.86-2.980.40251510.3562026X-RAY DIFFRACTION92.6
2.98-3.110.35531560.35791978X-RAY DIFFRACTION92.39
3.11-3.280.33351420.3572050X-RAY DIFFRACTION92.89
3.28-3.480.38111520.35362023X-RAY DIFFRACTION92.8
3.48-3.750.32641480.33082012X-RAY DIFFRACTION92.93
3.75-4.130.33981510.30552033X-RAY DIFFRACTION92.79
4.13-4.720.32671500.27532036X-RAY DIFFRACTION92.97
4.73-5.950.29941420.27472026X-RAY DIFFRACTION93.36
5.96-79.830.27741480.24352022X-RAY DIFFRACTION92.62

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