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- PDB-7bq4: X-ray structure of human PPARalpha ligand binding domain-eicosape... -

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Basic information

Entry
Database: PDB / ID: 7bq4
TitleX-ray structure of human PPARalpha ligand binding domain-eicosapentaenoic acid (EPA)-SRC1 coactivator peptide co-crystals obtained by delipidation and co-crystallization
Components
  • 15-meric peptide from Nuclear receptor coactivator 1
  • Peroxisome 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 / negative regulation of cell growth involved in cardiac muscle cell development / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process ...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 / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / 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 / negative regulation of glycolytic process / ubiquitin conjugating enzyme binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of fatty acid metabolic process / DNA-binding transcription activator activity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / 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 / epidermis development / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / phosphatase binding / response to retinoic acid / positive regulation of lipid biosynthetic process / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone H4K16 acetyltransferase activity / cellular response to hormone stimulus / 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 / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / intracellular receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of reactive oxygen species biosynthetic process / estrogen receptor signaling pathway / nitric oxide metabolic process / negative regulation of blood pressure / positive regulation of adipose tissue development / hormone-mediated signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha / MDM2/MDM4 family protein binding / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of cytokine production involved in inflammatory response / positive regulation of gluconeogenesis / positive regulation of neuron differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / hippocampus development / response to progesterone / cellular response to starvation / nuclear receptor binding / gluconeogenesis / fatty acid metabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / response to insulin / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway
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 / Nuclear receptor coactivators bHLH domain / 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 / 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
Similarity search - Domain/homology
5,8,11,14,17-EICOSAPENTAENOIC ACID / Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsKamata, S. / 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
DepositionMar 23, 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
B: 15-meric peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0994
Polymers32,7042
Non-polymers3952
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-10 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.969, 61.482, 53.116
Angle α, β, γ (deg.)90.000, 106.760, 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: Protein/peptide 15-meric peptide from Nuclear receptor coactivator 1


Mass: 1848.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-EPA / 5,8,11,14,17-EICOSAPENTAENOIC ACID


Mass: 302.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#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.: 103 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1 M Tris (pH 8.0), 30 %(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 7, 2020 / 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: 1.62→43.06 Å / Num. obs: 34634 / % possible obs: 98.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.021 / Rrim(I) all: 0.04 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.62-1.650.3093.416810.9030.2030.37198.3
8.87-43.060.01321810.0080.01696.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.45 Å39.19 Å
Translation5.45 Å39.19 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: 3SP6

3sp6


Resolution: 1.62→39.189 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 21.13
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2145 1640 4.96 %
Rwork0.188 --
obs0.1893 34624 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.63 Å2 / Biso mean: 22.7557 Å2 / Biso min: 10.56 Å2
Refinement stepCycle: final / Resolution: 1.62→39.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 65 103 2325
Biso mean--32.23 25.04 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082266
X-RAY DIFFRACTIONf_angle_d0.9663046
X-RAY DIFFRACTIONf_chiral_restr0.051346
X-RAY DIFFRACTIONf_plane_restr0.006389
X-RAY DIFFRACTIONf_dihedral_angle_d10.8211388
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.62-1.64420.28051440.2394259992
1.6442-1.66990.26511540.2224270095
1.6699-1.69730.23841360.2249273095
1.6973-1.72650.28561390.2116273695
1.7265-1.75790.23581540.2083266794
1.7579-1.79170.21771650.1991272296
1.7917-1.82830.25411510.2017269295
1.8283-1.86810.24991310.1949276395
1.8681-1.91150.22071620.1931269496
1.9115-1.95930.27051500.1904276696
1.9593-2.01230.22621420.1967267795
2.0123-2.07150.23521360.1953273495
2.0715-2.13840.20171280.1912275895
2.1384-2.21480.28051350.1873264493
2.2148-2.30340.21351200.1917267092
2.3034-2.40830.19551220.1871274096
2.4083-2.53520.26221550.2004279196
2.5352-2.6940.21791040.201277297
2.694-2.9020.22291390.2078278297
2.902-3.19390.24921690.2003274196
3.1939-3.65570.16931380.1854277196
3.6557-4.60470.1681470.1521267394
4.6047-39.1890.18761490.1665280497

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