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- PDB-7sqa: PPAR gamma LBD bound to SR10221 and SMRT corepressor motif -

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Basic information

Entry
Database: PDB / ID: 7sqa
TitlePPAR gamma LBD bound to SR10221 and SMRT corepressor motif
Components
  • Nuclear receptor corepressor 2
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Inverse agonist / Nuclear receptor / Ligand binding domain / corepressor
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / 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 / Notch binding ...Loss of MECP2 binding ability to the NCoR/SMRT complex / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / 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 / Notch binding / 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 / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / Notch-HLH transcription pathway / 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 / Regulation of MECP2 expression and activity / 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 / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / lactation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / cerebellum development / negative regulation of miRNA transcription / peptide binding / SUMOylation of transcription cofactors / enzyme activator activity / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / HDACs deacetylate histones / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / regulation of blood pressure / NOTCH1 Intracellular Domain Regulates Transcription / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / RNA polymerase II transcription regulator complex / nuclear matrix
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / Peroxisome proliferator-activated receptor / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / : / Homeobox-like domain superfamily / 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
Similarity search - Domain/homology
Chem-A8R / Peroxisome proliferator-activated receptor gamma / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsFrkic, R.L. / Pederick, J.L. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: PPAR gamma Corepression Involves Alternate Ligand Conformation and Inflation of H12 Ensembles.
Authors: Frkic, R.L. / Pederick, J.L. / Horsfall, A.J. / Jovcevski, B. / Crame, E.E. / Kowalczyk, W. / Pukala, T.L. / Chang, M.R. / Zheng, J. / Blayo, A.L. / Abell, A.D. / Kamenecka, T.M. / Harbort, ...Authors: Frkic, R.L. / Pederick, J.L. / Horsfall, A.J. / Jovcevski, B. / Crame, E.E. / Kowalczyk, W. / Pukala, T.L. / Chang, M.R. / Zheng, J. / Blayo, A.L. / Abell, A.D. / Kamenecka, T.M. / Harbort, J.S. / Harmer, J.R. / Griffin, P.R. / Bruning, J.B.
History
DepositionNov 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 31, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Nuclear receptor corepressor 2
D: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9236
Polymers71,8014
Non-polymers1,1222
Water3,441191
1
A: Peroxisome proliferator-activated receptor gamma
D: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4623
Polymers35,9012
Non-polymers5611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-9 kcal/mol
Surface area14120 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor gamma
C: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4623
Polymers35,9012
Non-polymers5611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-6 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.143, 59.700, 92.938
Angle α, β, γ (deg.)90.000, 105.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33300.520 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: Protein/peptide Nuclear receptor corepressor 2 / N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid hormone ...N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / T3 receptor-associating factor / TRAC / Thyroid- / retinoic-acid-receptor-associated corepressor


Mass: 2599.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y618
#3: Chemical ChemComp-A8R / (2S)-2-{5-[(5-{[(1S)-1-(4-tert-butylphenyl)ethyl]carbamoyl}-2,3-dimethyl-1H-indol-1-yl)methyl]-2-chlorophenoxy}propanoic acid


Mass: 561.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H37ClN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 28% PEG 8,000, 0.1M Ammonium sulphate, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.499→43.87 Å / Num. obs: 22167 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.092 / Rrim(I) all: 0.169 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.63.41.158837624940.4310.7311.3730.898.6
9.01-43.873.30.04616565000.9950.030.05515.795.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6pdz

6pdz


Resolution: 2.499→41.884 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 1137 5.17 %
Rwork0.2338 20875 -
obs0.2366 22012 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.84 Å2 / Biso mean: 64.7404 Å2 / Biso min: 15.63 Å2
Refinement stepCycle: final / Resolution: 2.499→41.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4299 0 80 191 4570
Biso mean--64.96 50.91 -
Num. residues----542
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.499-2.61230.38051270.3053260598
2.6123-2.750.36611240.3181257396
2.75-2.92230.33091400.28522652100
2.9223-3.14790.4021460.27652651100
3.1479-3.46450.29531510.2598259698
3.4645-3.96550.29571300.2327244892
3.9655-4.99480.24711670.1827265199
4.9948-41.8840.23241520.2039269998
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)
11.3017-2.79571.24486.0107-2.75772.25610.40640.0046-0.3295-0.743-0.02390.80790.4615-0.1794-0.28540.5396-0.097-0.08320.35370.01940.50280.2996-10.3379-43.6121
21.6423-1.68480.44452.525-1.0712.2045-0.0317-0.2645-0.02370.17660.16930.1882-0.1485-0.3643-0.1210.3532-0.07350.03310.3529-0.04590.28153.3871-6.9269-31.152
32.0076-0.7576-0.26312.43981.51973.5488-0.174-0.31210.23880.60010.1172-0.05320.12670.65430.10430.4416-0.035-0.02420.37040.03730.27331.796-6.8221-7.899
42.1131-2.0824-0.68657.21880.58784.34380.31430.0657-0.10340.5948-0.516-0.0064-0.12970.5374-0.25810.7409-0.0676-0.01240.4395-0.16750.309318.498110.549111.725
50.9509-0.39450.16892.40411.37593.6971-0.04420.05380.1018-0.1166-0.10880.3075-0.5982-0.27330.08780.4181-0.00790.00070.3574-0.00550.323220.50210.2907-12.2844
64.18112.0707-3.69543.65420.67075.64260.0433-0.07230.83730.18610.47380.28420.67940.31320.22521.4528-0.0112-0.13080.34540.01090.570829.301516.3615-16.4803
74.49040.9327-2.51892.92060.76564.2454-0.2429-0.1762-0.1080.37260.04070.36680.3909-0.2570.71580.37490.13510.31640.79020.14180.4944-12.1254-14.0006-24.1583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 200 through 276 )A200 - 276
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 461 )A277 - 461
3X-RAY DIFFRACTION3chain 'B' and (resid 202 through 251 )B202 - 251
4X-RAY DIFFRACTION4chain 'B' and (resid 252 through 276 )B252 - 276
5X-RAY DIFFRACTION5chain 'B' and (resid 277 through 461 )B277 - 461
6X-RAY DIFFRACTION6chain 'C' and (resid 2338 through 2352 )C0
7X-RAY DIFFRACTION7chain 'D' and (resid 2339 through 2350 )D0

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