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- PDB-9iwl: X-ray structure of human PPARalpha ligand binding domain-intrinsi... -

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Basic information

Entry
Database: PDB / ID: 9iwl
TitleX-ray structure of human PPARalpha ligand binding domain-intrinsic fatty acid (E. coli origin)-CBP coactivator peptide co-crystals obtained by cross-seeding
Components
  • CREB-binding protein
  • Peroxisome proliferator-activated receptor alpha
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR / Coactivator / CBP
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / negative regulation of cell growth involved in cardiac muscle cell development / regulation of fatty acid metabolic process ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / negative regulation of cell growth involved in cardiac muscle cell development / regulation of fatty acid metabolic process / negative regulation of appetite / peptide lactyltransferase (CoA-dependent) activity / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / lipoprotein metabolic process / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / negative regulation of leukocyte cell-cell adhesion / histone H3K18 acetyltransferase activity / : / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / negative regulation of glycolytic process / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Nuclear events mediated by NFE2L2 / Regulation of gene expression by Hypoxia-inducible Factor / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / embryonic digit morphogenesis / protein acetylation / positive regulation of fatty acid metabolic process / DNA-binding transcription activator activity / Notch-HLH transcription pathway / NFAT protein binding / Formation of paraxial mesoderm / acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of cell death genes / negative regulation of cholesterol storage / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / homeostatic process / histone acetyltransferase activity / positive regulation of ATP biosynthetic process / nuclear steroid receptor activity / : / histone acetyltransferase complex / negative regulation of macrophage derived foam cell differentiation / protein-lysine-acetyltransferase activity / epidermis development / cAMP/PKA signal transduction / canonical NF-kappaB signal transduction / Attenuation phase / positive regulation of lipid biosynthetic process / phosphatase binding / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / histone acetyltransferase / regulation of cellular response to heat / positive regulation of double-strand break repair via homologous recombination / negative regulation of blood pressure / intracellular receptor signaling pathway / nitric oxide metabolic process / negative regulation of reactive oxygen species biosynthetic process / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / cellular response to nutrient levels / negative regulation of cytokine production involved in inflammatory response / response to nutrient / Transcriptional and post-translational regulation of MITF-M expression and activity / MDM2/MDM4 family protein binding / BMAL1:CLOCK,NPAS2 activates circadian expression / CD209 (DC-SIGN) signaling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of gluconeogenesis / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : ...Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Peroxisome proliferator-activated receptor / Nuclear receptor coactivator, interlocking / : / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PALMITIC ACID / Peroxisome proliferator-activated receptor alpha / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKamata, S. / Honda, A. / Yashiro, S. / Komori, Y. / Shimamura, A. / Hosoda, A. / Oyama, T. / Ishii, I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K15049 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

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor alpha
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1504
Polymers32,8012
Non-polymers3492
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-9 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.910, 60.992, 53.948
Angle α, β, γ (deg.)90.00, 110.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator-activated receptor alpha


Mass: 30856.053 Da / Num. of mol.: 1
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 CREB-binding protein / Histone lysine acetyltransferase CREBBP / Protein lactyltransferas CREBBP / Protein-lysine ...Histone lysine acetyltransferase CREBBP / Protein lactyltransferas CREBBP / Protein-lysine acetyltransferase CREBBP


Mass: 1945.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q92793, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1M Tris (pH 8.5), 30% PEG 4000, 0.2M Sodium acetate trihydrate

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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: Jun 24, 2024 / 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: 2.09→42.06 Å / Num. obs: 16145 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Net I/σ(I): 17.7 / Num. measured all: 53408
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3 / Num. unique obs: 1243 / CC1/2: 0.843 / Rpim(I) all: 0.248 / Rrim(I) all: 0.459

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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: 2.09→27.874 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1418 4.67 %
Rwork0.178 --
obs0.1807 16128 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→27.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 24 34 2224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012248
X-RAY DIFFRACTIONf_angle_d1.1023021
X-RAY DIFFRACTIONf_dihedral_angle_d13.2371383
X-RAY DIFFRACTIONf_chiral_restr0.052345
X-RAY DIFFRACTIONf_plane_restr0.006382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.16470.27661240.23022849X-RAY DIFFRACTION93
2.1647-2.25130.30431610.22262915X-RAY DIFFRACTION96
2.2513-2.35370.28461330.20972881X-RAY DIFFRACTION96
2.3537-2.47780.30591290.21112873X-RAY DIFFRACTION95
2.4778-2.63290.2491640.20432893X-RAY DIFFRACTION96
2.6329-2.8360.27041650.19182857X-RAY DIFFRACTION96
2.836-3.12110.25561150.20342930X-RAY DIFFRACTION96
3.1211-3.57190.2281330.18652923X-RAY DIFFRACTION97
3.5719-4.49710.24271490.14532934X-RAY DIFFRACTION96
4.4971-27.8740.16611450.14662900X-RAY DIFFRACTION96

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