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- PDB-6lxc: X-ray structure of human PPARalpha ligand binding domain-saroglit... -

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Basic information

Entry
Database: PDB / ID: 6lxc
TitleX-ray structure of human PPARalpha ligand binding domain-saroglitazar co-crystals obtained by delipidation and cross-seeding
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 / lipoprotein metabolic process / positive regulation of fatty acid oxidation / 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 / positive regulation of fatty acid metabolic process / DNA-binding transcription activator activity / 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 / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / response to insulin / 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-EWR / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsKamata, S. / Honda, A. / Ishikawa, R. / Akahane, M. / 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
DepositionFeb 10, 2020Deposition 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 29, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,2962
Polymers30,8561
Non-polymers4401
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12560 Å2
Unit cell
Length a, b, c (Å)44.688, 62.484, 53.481
Angle α, β, γ (deg.)90.000, 106.320, 90.000
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: Chemical ChemComp-EWR / (2S)-2-ethoxy-3-[4-[2-[2-methyl-5-(4-methylsulfanylphenyl)pyrrol-1-yl]ethoxy]phenyl]propanoic acid


Mass: 439.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1M Tris (pH 8.5), 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: May 19, 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: 2.03→39.66 Å / Num. obs: 18306 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.083.60.2514.813080.9510.1550.29698.1
9.08-39.663.10.01620810.010.01995.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.03 Å39.66 Å
Translation2.03 Å39.66 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575-000refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VI8

3vi8


Resolution: 2.03→32.896 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 23.27
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2173 1758 5.08 %
Rwork0.1926 --
obs0.1938 18289 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.79 Å2 / Biso mean: 30.6349 Å2 / Biso min: 13.81 Å2
Refinement stepCycle: final / Resolution: 2.03→32.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 59 71 2174
Biso mean--26.68 29.27 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032149
X-RAY DIFFRACTIONf_angle_d0.542901
X-RAY DIFFRACTIONf_chiral_restr0.036329
X-RAY DIFFRACTIONf_plane_restr0.003370
X-RAY DIFFRACTIONf_dihedral_angle_d12.2871306
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0301-2.0850.29441320.236241194
2.085-2.14630.30031330.2212257296
2.1463-2.21560.3321320.2275250596
2.2156-2.29470.26611290.2157250897
2.2947-2.38660.26661530.2139259297
2.3866-2.49520.25071400.2083250997
2.4952-2.62670.21861280.2162255197
2.6267-2.79120.24141300.2239256597
2.7912-3.00650.24511560.2148247796
3.0065-3.30880.24941250.2245246293
3.3088-3.7870.20321220.1736255297
3.787-4.76890.15381280.1498260599
4.7689-32.8960.15841500.162256599

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