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- PDB-6l96: Structure of PPARalpha-LBD/pemafibrate/SRC1 peptide -

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Basic information

Entry
Database: PDB / ID: 6l96
TitleStructure of PPARalpha-LBD/pemafibrate/SRC1 peptide
Components
  • Peroxisome proliferator-activated receptor alpha
  • SRC1 coactivator peptide
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / regulation of ketone metabolic process / regulation of fatty acid metabolic process / cellular response to fructose stimulus / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / behavioral response to nicotine ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / regulation of ketone metabolic process / regulation of fatty acid metabolic process / cellular response to fructose stimulus / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / behavioral response to nicotine / lipoprotein metabolic process / positive regulation of fatty acid oxidation / negative regulation of hepatocyte apoptotic process / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of triglyceride storage / nuclear steroid receptor activity / nitric oxide metabolic process / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / cellular response to Thyroglobulin triiodothyronine / negative regulation of macrophage derived foam cell differentiation / Synthesis of bile acids and bile salts / negative regulation of cytokine production involved in inflammatory response / epidermis development / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / phosphatase binding / nuclear retinoid X receptor binding / progesterone receptor signaling pathway / response to retinoic acid / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / cellular response to hormone stimulus / estrous cycle / Recycling of bile acids and salts / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of blood pressure / negative regulation of signaling receptor activity / negative regulation of reactive oxygen species biosynthetic process / estrogen receptor signaling pathway / positive regulation of adipose tissue development / : / hormone-mediated signaling pathway / MDM2/MDM4 family protein binding / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / response to nutrient / positive regulation of gluconeogenesis / regulation of cellular response to insulin stimulus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cerebellum development / positive regulation of neuron differentiation / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / : / cellular response to starvation / hippocampus development / response to progesterone / nuclear receptor binding / gluconeogenesis / fatty acid metabolic process / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to insulin / SUMOylation of intracellular receptors
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-P7F / Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKawasaki, M. / Kambe, A. / Yamamoto, Y. / Arulmozhira, S. / Ito, S. / Nakagawa, Y. / Tokiwa, H. / Nakano, S. / Shimano, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science18K14391 Japan
Japan Society for the Promotion of Science16K18688 Japan
CitationJournal: Int J Mol Sci / Year: 2020
Title: Elucidation of Molecular Mechanism of a Selective PPAR alpha Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations.
Authors: Kawasaki, M. / Kambe, A. / Yamamoto, Y. / Arulmozhiraja, S. / Ito, S. / Nakagawa, Y. / Tokiwa, H. / Nakano, S. / Shimano, H.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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
B: Peroxisome proliferator-activated receptor alpha
C: SRC1 coactivator peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8355
Polymers63,8543
Non-polymers9812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-19 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.736, 82.736, 177.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A10 - 273
2010B10 - 273

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Components

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


Mass: 31131.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA, NR1C1, PPAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Protein/peptide SRC1 coactivator peptide


Mass: 1591.880 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: Q15788*PLUS
#3: Chemical ChemComp-P7F / (2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic acid


Mass: 490.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.2 M ammonium sulfate and 0.1M bis-tris-HCl (pH 6.5)

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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 2M / Detector: PIXEL / Date: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→45.7 Å / Num. obs: 22457 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.8
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1107 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYK

5hyk


Resolution: 3.2→45.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 23.012 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25272 544 4.5 %RANDOM
Rwork0.18727 ---
obs0.19025 11627 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 3.2→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 72 0 4196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174105
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.6565760
X-RAY DIFFRACTIONr_angle_other_deg1.1931.5949524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66823.398206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.18915790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7171519
X-RAY DIFFRACTIONr_chiral_restr0.0690.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024644
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02849
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.61310.7682071
X-RAY DIFFRACTIONr_mcbond_other8.60910.7672070
X-RAY DIFFRACTIONr_mcangle_it12.73216.1322580
X-RAY DIFFRACTIONr_mcangle_other12.7316.1332581
X-RAY DIFFRACTIONr_scbond_it8.83611.1572201
X-RAY DIFFRACTIONr_scbond_other8.83511.1592202
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.36416.5023179
X-RAY DIFFRACTIONr_long_range_B_refined16.2444819
X-RAY DIFFRACTIONr_long_range_B_other16.2434820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.201→3.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 39 -
Rwork0.259 851 -
obs--100 %

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