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- PDB-7bpy: X-ray structure of human PPARalpha ligand binding domain-clofibri... -

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Basic information

Entry
Database: PDB / ID: 7bpy
TitleX-ray structure of human PPARalpha ligand binding domain-clofibric acid-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 / regulation of ketone metabolic process / cellular response to fructose stimulus / 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 / regulation of ketone metabolic process / cellular response to fructose stimulus / 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 / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / positive regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / cellular response to hormone stimulus / 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 / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / 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 / : / MDM2/MDM4 family protein binding / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / regulation of cellular response to insulin stimulus / response to nutrient / 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 / cellular response to starvation / response to progesterone / 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 / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression
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
2-(4-chloranylphenoxy)-2-methyl-propanoic 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: 2.09 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
C: Peroxisome proliferator-activated receptor alpha
D: 15-meric peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2678
Polymers65,4084
Non-polymers8594
Water1,856103
1
A: Peroxisome proliferator-activated receptor alpha
B: 15-meric peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1344
Polymers32,7042
Non-polymers4292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area13520 Å2
MethodPISA
2
C: Peroxisome proliferator-activated receptor alpha
D: 15-meric peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1344
Polymers32,7042
Non-polymers4292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-9 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.535, 101.646, 61.425
Angle α, β, γ (deg.)90.000, 101.820, 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.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical
ChemComp-E0O / 2-(4-chloranylphenoxy)-2-methyl-propanoic acid


Mass: 214.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H11ClO3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1 M Tris (pH 8.5), 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: 2.09→47.32 Å / Num. obs: 42307 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 30.46 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
2.09-2.153.60.344432790.8990.2110.40497.6
9.11-47.323.40.01352110.0080.01695.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.09 Å38.58 Å
Translation2.09 Å38.58 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: 2.09→38.576 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 23.02
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2155 1940 4.74 %
Rwork0.1933 --
obs0.1943 42303 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.12 Å2 / Biso mean: 36.8841 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: final / Resolution: 2.09→38.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 96 103 4663
Biso mean--52.94 31.9 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054623
X-RAY DIFFRACTIONf_angle_d0.7046240
X-RAY DIFFRACTIONf_chiral_restr0.04711
X-RAY DIFFRACTIONf_plane_restr0.004794
X-RAY DIFFRACTIONf_dihedral_angle_d13.3012808
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.09-2.11550.27031400.24277995
2.1155-2.14230.27321390.2322275496
2.1423-2.17050.27741290.2333282097
2.1705-2.20020.26891740.2171275596
2.2002-2.23160.2721520.2363273596
2.2316-2.2650.27321350.2196278196
2.265-2.30030.27741480.2233269796
2.3003-2.3380.24111180.2136283296
2.338-2.37840.27871560.2163269796
2.3784-2.42160.25221240.2098284095
2.4216-2.46820.26091450.2095270596
2.4682-2.51850.26271230.2223277396
2.5185-2.57330.27181300.2086277495
2.5733-2.63310.29981410.2186276295
2.6331-2.6990.18741340.2055273496
2.699-2.77190.23191240.2086280996
2.7719-2.85350.26861080.2165279597
2.8535-2.94550.23161380.2305287798
2.9455-3.05080.29361280.2276282998
3.0508-3.17290.27081510.2312279197
3.1729-3.31720.23371460.2236278698
3.3172-3.4920.21191610.2063281797
3.492-3.71060.19411670.1834274797
3.7106-3.99680.17631550.168280597
3.9968-4.39850.18551550.1507277597
4.3985-5.03380.18121050.1521282597
5.0338-6.33750.17561070.1755286798
6.3375-38.5760.12321460.1427275696

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