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- PDB-9iwk: X-ray structure of human PPARgamma ligand binding domain-NCoR2 co... -

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Basic information

Entry
Database: PDB / ID: 9iwk
TitleX-ray structure of human PPARgamma ligand binding domain-NCoR2 corepressor peptide co-crystals obtained by co-crystallization
Components
  • Isoform 1 of Peroxisome proliferator-activated receptor gamma
  • Nuclear receptor corepressor 2
KeywordsTRANSCRIPTION / Nuclear receptor / Corepressor / PPAR / NCoR
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / estrous cycle / nuclear retinoid X receptor binding ...Loss of MECP2 binding ability to the NCoR/SMRT complex / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / estrous cycle / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / cerebellum development / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / PPARA activates gene expression / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / NOTCH1 Intracellular Domain Regulates Transcription / Transcriptional regulation of white adipocyte differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / nuclear matrix / HCMV Early Events / transcription corepressor activity / response to estradiol / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / nuclear body / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / membrane
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Isoform 1 of Peroxisome proliferator-activated receptor gamma / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKamata, S. / Honda, A. / Masuda, R. / Oota, M. / Namatame, R. / Machida, Y. / Uchii, K. / Shiiyama, Y. / Oyama, T. / Ishii, I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K16359 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: Antioxidants / Year: 2025
Title: Competitive Ligand-Induced Recruitment of Coactivators to Specific PPAR alpha / delta / gamma Ligand-Binding Domains Revealed by Dual-Emission FRET and X-Ray Diffraction of Cocrystals.
Authors: Kamata, S. / Honda, A. / Yashiro, S. / Kaneko, C. / Komori, Y. / Shimamura, A. / Masuda, R. / Oyama, T. / Ishii, I.
History
DepositionJul 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of Peroxisome proliferator-activated receptor gamma
B: Nuclear receptor corepressor 2
C: Isoform 1 of Peroxisome proliferator-activated receptor gamma
D: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)68,9264
Polymers68,9264
Non-polymers00
Water00
1
A: Isoform 1 of Peroxisome proliferator-activated receptor gamma
B: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)34,4632
Polymers34,4632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area12570 Å2
MethodPISA
2
C: Isoform 1 of Peroxisome proliferator-activated receptor gamma
D: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)34,4632
Polymers34,4632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-10 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.299, 60.054, 92.828
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoform 1 of Peroxisome proliferator-activated receptor gamma / PPAR-gamma


Mass: 31862.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P37231-2
#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 / Fragment: UNP residues 2346-2367 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y618
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M Tris (pH 8.5), 30% PEG 8000, 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2021 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→44.69 Å / Num. obs: 24392 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.024 / Rrim(I) all: 0.045 / Net I/σ(I): 16.1 / Num. measured all: 85105
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2536 / CC1/2: 0.897 / Rpim(I) all: 0.244 / Rrim(I) all: 0.467 / % possible all: 97.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX(1.11.1_2575-000)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→44.084 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 33.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 2294 4.93 %
Rwork0.2382 --
obs0.2397 24381 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→44.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 0 0 3881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023940
X-RAY DIFFRACTIONf_angle_d0.4075307
X-RAY DIFFRACTIONf_dihedral_angle_d13.5952432
X-RAY DIFFRACTIONf_chiral_restr0.035626
X-RAY DIFFRACTIONf_plane_restr0.003670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4303-2.48310.32321240.30612757X-RAY DIFFRACTION96
2.4831-2.54090.34661580.30212777X-RAY DIFFRACTION98
2.5409-2.60440.35051300.28542804X-RAY DIFFRACTION97
2.6044-2.67480.31391100.28362827X-RAY DIFFRACTION98
2.6748-2.75350.31421660.28462763X-RAY DIFFRACTION97
2.7535-2.84240.38041360.27952820X-RAY DIFFRACTION98
2.8424-2.9440.28841230.30352773X-RAY DIFFRACTION98
2.944-3.06180.32961480.30272834X-RAY DIFFRACTION97
3.0618-3.20110.31751410.28782770X-RAY DIFFRACTION98
3.2011-3.36980.33671430.28062751X-RAY DIFFRACTION96
3.3698-3.58090.33951080.26942644X-RAY DIFFRACTION92
3.5809-3.85720.29841530.23142779X-RAY DIFFRACTION98
3.8572-4.24510.21731470.21692801X-RAY DIFFRACTION99
4.2451-4.85870.24951640.20282775X-RAY DIFFRACTION98
4.8587-6.11880.24831760.21952748X-RAY DIFFRACTION97
6.1188-44.0840.17791670.18482624X-RAY DIFFRACTION93

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