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- PDB-6a6p: Crystal Structure of Peroxisome Proliferator-Activated Receptor D... -

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Basic information

Entry
Database: PDB / ID: 6a6p
TitleCrystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd)LBD in Complex with DN003316
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsSTRUCTURAL PROTEIN / PPARdelta / complex / nuclear receptor / peroxisome proliferator-activated receptor family / ligand binding domain (LBD)
Function / homology
Function and homology information


fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / regulation of skeletal muscle satellite cell proliferation / axon ensheathment / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / regulation of skeletal muscle satellite cell proliferation / axon ensheathment / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / negative regulation of myoblast differentiation / Carnitine metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / fatty acid beta-oxidation / positive regulation of fatty acid metabolic process / cell-substrate adhesion / negative regulation of cholesterol storage / cellular response to nutrient levels / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / fatty acid transport / adipose tissue development / energy homeostasis / embryo implantation / cholesterol metabolic process / hormone-mediated signaling pathway / fatty acid metabolic process / negative regulation of miRNA transcription / phosphatidylinositol 3-kinase/protein kinase B signal transduction / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / lipid binding / apoptotic process / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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, beta / Peroxisome proliferator-activated receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Peroxisome proliferator-activated receptor, beta / Peroxisome proliferator-activated receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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-9RF / heptyl beta-D-glucopyranoside / Chem-PE3 / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChin, J.W. / Cho, S.J. / Song, J.Y. / Ha, J.H.
CitationJournal: To Be Published
Title: Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd)LBD in Complex with DN003316
Authors: Chin, J.W. / Cho, S.J. / Song, J.Y. / Ha, J.H.
History
DepositionJun 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 delta
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4158
Polymers61,7082
Non-polymers2,7076
Water4,017223
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2074
Polymers30,8541
Non-polymers1,3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-0 kcal/mol
Surface area13220 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2074
Polymers30,8541
Non-polymers1,3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-0 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.605, 95.749, 96.936
Angle α, β, γ (deg.)90.00, 97.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator-activated receptor delta / / PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member ...PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member 2 / Peroxisome proliferator-activated receptor beta / PPAR-beta


Mass: 30853.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181
#2: Chemical ChemComp-9RF / {2-methyl-4-[({5-[4-(trifluoromethyl)phenyl]-1,3,4-thiadiazol-2-yl}methyl)sulfanyl]phenoxy}acetic acid


Mass: 440.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15F3N2O3S2
#3: Sugar ChemComp-B7G / heptyl beta-D-glucopyranoside / HEPTYL-BETA-D-GLUCOPYRANOSIDE / heptyl beta-D-glucoside / heptyl D-glucoside / heptyl glucoside


Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26O6
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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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: 58.62 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion / pH: 6.5 / Details: 0.2~0.3M Sodium flouride, 0.1M MES(pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 41153 / % possible obs: 98.34 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.1024 / Net I/σ(I): 19.01
Reflection shellResolution: 2.1→2.14 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U3R

5u3r


Resolution: 2.1→38.201 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.2278 2025 4.92 %
Rwork0.1936 --
obs0.1953 41144 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 182 223 4690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084576
X-RAY DIFFRACTIONf_angle_d0.9946155
X-RAY DIFFRACTIONf_dihedral_angle_d17.1652747
X-RAY DIFFRACTIONf_chiral_restr0.054689
X-RAY DIFFRACTIONf_plane_restr0.007759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.33181170.29842398X-RAY DIFFRACTION85
2.1525-2.21070.29771340.26972799X-RAY DIFFRACTION98
2.2107-2.27580.27551370.2372753X-RAY DIFFRACTION98
2.2758-2.34920.26791490.22052806X-RAY DIFFRACTION99
2.3492-2.43320.24091520.21272783X-RAY DIFFRACTION99
2.4332-2.53060.24321630.21072802X-RAY DIFFRACTION99
2.5306-2.64570.22641570.21432852X-RAY DIFFRACTION100
2.6457-2.78520.25891470.20772784X-RAY DIFFRACTION100
2.7852-2.95960.28761790.21072815X-RAY DIFFRACTION100
2.9596-3.1880.24921470.21342826X-RAY DIFFRACTION100
3.188-3.50860.24991190.19862862X-RAY DIFFRACTION100
3.5086-4.01580.20841480.17422879X-RAY DIFFRACTION100
4.0158-5.05770.1891420.1542847X-RAY DIFFRACTION100
5.0577-38.20710.18241340.17662913X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.8173 Å / Origin y: 25.7103 Å / Origin z: 24.3599 Å
111213212223313233
T0.2338 Å2-0.0018 Å2-0.0032 Å2-0.2862 Å2-0.0092 Å2--0.2099 Å2
L0.3994 °20.09 °2-0.0414 °2-0.9581 °2-0.2966 °2--0.3141 °2
S0.0022 Å °-0.0216 Å °0 Å °-0.0404 Å °0.0177 Å °-0.0206 Å °-0.039 Å °0.0638 Å °-0.0168 Å °
Refinement TLS groupSelection details: all

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