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- PDB-6kb2: X-ray structure of human PPARalpha ligand binding domain-Wy14643 ... -

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Basic information

Entry
Database: PDB / ID: 6kb2
TitleX-ray structure of human PPARalpha ligand binding domain-Wy14643 co-crystals obtained by soaking
ComponentsPeroxisome proliferator-activated receptor alpha
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR
Function / homology
Function and homology information


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 / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite / negative regulation of hepatocyte apoptotic process ...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 / 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 / lipoprotein metabolic process / behavioral response to nicotine / negative regulation of leukocyte cell-cell adhesion / negative regulation of glycolytic process / ubiquitin conjugating enzyme binding / mitogen-activated protein kinase kinase kinase binding / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / 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 / epidermis development / phosphatase binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of blood pressure / intracellular receptor signaling pathway / nitric oxide metabolic process / negative regulation of reactive oxygen species biosynthetic process / hormone-mediated signaling pathway / : / Regulation of lipid metabolism by PPARalpha / MDM2/MDM4 family protein binding / peroxisome proliferator activated receptor signaling pathway / response to nutrient / positive regulation of gluconeogenesis / negative regulation of cytokine production involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / cellular response to starvation / gluconeogenesis / SUMOylation of intracellular receptors / circadian regulation of gene expression / wound healing / Heme signaling / negative regulation of transforming growth factor beta receptor signaling pathway / fatty acid metabolic process / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / response to insulin / Cytoprotection by HMOX1 / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / nuclear receptor activity / : / heart development / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / lipid binding / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / Peroxisome proliferator-activated receptor / : / 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 ...Peroxisome proliferator-activated receptor alpha / Peroxisome proliferator-activated receptor / : / 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-WY1 / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsKamata, S. / Suda, K. / Saito, K. / Oyama, T. / Ishii, I.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H05107 Japan
CitationJournal: Iscience / Year: 2020
Title: PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates.
Authors: Kamata, S. / Oyama, T. / Saito, K. / Honda, A. / Yamamoto, Y. / Suda, K. / Ishikawa, R. / Itoh, T. / Watanabe, Y. / Shibata, T. / Uchida, K. / Suematsu, M. / Ishii, I.
History
DepositionJun 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5043
Polymers30,8561
Non-polymers6482
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12720 Å2
Unit cell
Length a, b, c (Å)45.164, 62.681, 53.667
Angle α, β, γ (deg.)90.000, 105.560, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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


Mass: 30856.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Chemical ChemComp-WY1 / 2-({4-CHLORO-6-[(2,3-DIMETHYLPHENYL)AMINO]PYRIMIDIN-2-YL}SULFANYL)ACETIC ACID


Mass: 323.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1M HEPES (pH 7.0), 25%(w/v) PEG3350

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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: Mar 16, 2019 / 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: 1.95→43.51 Å / Num. obs: 20767 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.25 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.017 / Rrim(I) all: 0.033 / Net I/σ(I): 21.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-23.50.3443.114620.9440.2150.40798.3
8.94-43.513.30.0118121710.0070.01394

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å43.51 Å
Translation1.95 Å43.51 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VI8

3vi8


Resolution: 1.95→32.998 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 30.19
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.244 1991 4.99 %
Rwork0.2047 --
obs0.2066 20741 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.8705 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 42 36 2192
LS refinement shellResolution: 1.9501→1.9988 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3281 147 -
Rwork0.2839 2692 -
obs--96 %

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