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- PDB-9iwj: X-ray structure of human PPARalpha ligand binding domain-NCoR2 co... -

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Basic information

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


Loss of MECP2 binding ability to the NCoR/SMRT complex / positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / nuclear glucocorticoid receptor binding / negative regulation of cell growth involved in cardiac muscle cell development ...Loss of MECP2 binding ability to the NCoR/SMRT complex / positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / nuclear glucocorticoid receptor binding / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / negative regulation of androgen receptor signaling pathway / lipoprotein metabolic process / behavioral response to nicotine / negative regulation of leukocyte cell-cell adhesion / negative regulation of glycolytic process / ubiquitin conjugating enzyme binding / Notch binding / mitogen-activated protein kinase kinase kinase binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / Notch-HLH transcription pathway / NFAT protein binding / negative regulation of cholesterol storage / positive regulation of ATP biosynthetic process / nuclear steroid receptor activity / negative regulation of macrophage derived foam cell differentiation / Regulation of MECP2 expression and activity / epidermis development / phosphatase binding / estrous cycle / nuclear retinoid X receptor binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / negative regulation of blood pressure / negative regulation of reactive oxygen species biosynthetic process / nitric oxide metabolic process / hormone-mediated signaling pathway / lactation / : / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / MDM2/MDM4 family protein binding / response to nutrient / peroxisome proliferator activated receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / positive regulation of gluconeogenesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / cerebellum development / cellular response to starvation / gluconeogenesis / HDACs deacetylate histones / SUMOylation of intracellular receptors / circadian regulation of gene expression / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / wound healing / negative regulation of transforming growth factor beta receptor signaling pathway / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / fatty acid metabolic process / Cytoprotection by HMOX1 / response to insulin / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription coactivator binding / histone deacetylase binding / nuclear matrix / nuclear receptor activity / HCMV Early Events / : / transcription corepressor activity / response to estradiol / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / response to hypoxia / nuclear body
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Peroxisome proliferator-activated receptor alpha / SANT domain profile. / SANT domain / Myb domain / Peroxisome proliferator-activated receptor / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Peroxisome proliferator-activated receptor alpha / SANT domain profile. / SANT domain / Myb domain / Peroxisome proliferator-activated receptor / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / : / Nuclear hormone receptor / Homeobox-like domain superfamily / 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
Peroxisome proliferator-activated receptor alpha / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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)JP19am0101071 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: Peroxisome proliferator-activated receptor alpha
B: Peroxisome proliferator-activated receptor alpha
C: Peroxisome proliferator-activated receptor alpha
D: Peroxisome proliferator-activated receptor alpha
E: Nuclear receptor corepressor 2
F: Nuclear receptor corepressor 2
G: Nuclear receptor corepressor 2
H: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)133,8248
Polymers133,8248
Non-polymers00
Water00
1
A: Peroxisome proliferator-activated receptor alpha
E: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)33,4562
Polymers33,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area12890 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor alpha
F: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)33,4562
Polymers33,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area13050 Å2
MethodPISA
3
C: Peroxisome proliferator-activated receptor alpha
G: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)33,4562
Polymers33,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-8 kcal/mol
Surface area12960 Å2
MethodPISA
4
D: Peroxisome proliferator-activated receptor alpha
H: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)33,4562
Polymers33,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-10 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.730, 112.152, 122.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peroxisome proliferator-activated receptor alpha


Mass: 30856.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#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.: 4 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M HEPES (pH 7.0), 14% PEG 8000, 0.2M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 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: 2.48→48.88 Å / Num. obs: 49517 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.015 / Rrim(I) all: 0.039 / Net I/σ(I): 28.9 / Num. measured all: 329013
Reflection shellResolution: 2.48→2.56 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4469 / CC1/2: 0.947 / Rpim(I) all: 0.15 / Rrim(I) all: 0.392 / % possible all: 99.9

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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: 2.48→38.711 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 4867 5.17 %
Rwork0.2249 --
obs0.2265 49439 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→38.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7478 0 0 0 7478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027622
X-RAY DIFFRACTIONf_angle_d0.51210272
X-RAY DIFFRACTIONf_dihedral_angle_d13.8894656
X-RAY DIFFRACTIONf_chiral_restr0.0371195
X-RAY DIFFRACTIONf_plane_restr0.0031304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.50820.31951480.28592925X-RAY DIFFRACTION99
2.5082-2.53770.3051710.27882945X-RAY DIFFRACTION100
2.5377-2.56870.30661540.27843020X-RAY DIFFRACTION100
2.5687-2.60120.32831470.27562996X-RAY DIFFRACTION100
2.6012-2.63540.35181810.29942986X-RAY DIFFRACTION100
2.6354-2.67150.34811710.29092958X-RAY DIFFRACTION100
2.6715-2.70960.31881450.28532951X-RAY DIFFRACTION100
2.7096-2.75010.32241540.28282977X-RAY DIFFRACTION100
2.7501-2.7930.3151790.27792990X-RAY DIFFRACTION100
2.793-2.83880.29861460.26992982X-RAY DIFFRACTION100
2.8388-2.88770.34581870.27562963X-RAY DIFFRACTION100
2.8877-2.94020.32171540.28843023X-RAY DIFFRACTION100
2.9402-2.99680.39881650.29762956X-RAY DIFFRACTION100
2.9968-3.05790.31481640.3022969X-RAY DIFFRACTION100
3.0579-3.12440.32381670.2853002X-RAY DIFFRACTION100
3.1244-3.1970.34721580.29852991X-RAY DIFFRACTION100
3.197-3.27690.35181550.28452949X-RAY DIFFRACTION100
3.2769-3.36550.28171430.27182987X-RAY DIFFRACTION100
3.3655-3.46450.29431300.26433040X-RAY DIFFRACTION100
3.4645-3.57620.2661850.23852934X-RAY DIFFRACTION100
3.5762-3.70390.22191860.23272973X-RAY DIFFRACTION100
3.7039-3.85210.23931740.21242988X-RAY DIFFRACTION100
3.8521-4.02720.24091680.19962946X-RAY DIFFRACTION100
4.0272-4.23930.20991560.18432986X-RAY DIFFRACTION100
4.2393-4.50460.19571720.17943002X-RAY DIFFRACTION100
4.5046-4.85180.19011180.17752982X-RAY DIFFRACTION100
4.8518-5.33890.24081390.19323018X-RAY DIFFRACTION100
5.3389-6.10880.24551670.21632967X-RAY DIFFRACTION100
6.1088-7.68660.2252010.19782934X-RAY DIFFRACTION100
7.6866-38.7110.19451820.17152945X-RAY DIFFRACTION99

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