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- PDB-3gz9: Crystal Structure of Peroxisome Proliferator-Activated Receptor D... -

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Entry
Database: PDB / ID: 3gz9
TitleCrystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd) in Complex with a Full Agonist
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION / PPAR / PPAR delta / nuclear receptor fold / transcription regulation / hormone / growth factor receptor / complex / Activator / Alternative splicing / DNA-binding / Metal-binding / Nucleus / Receptor / Zinc / Zinc-finger
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 / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / 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 / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / Carnitine metabolism / negative regulation of myoblast differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / cell-substrate adhesion / fatty acid beta-oxidation / 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 / hormone-mediated signaling pathway / cholesterol metabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / fatty acid metabolic process / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / 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 / positive regulation of gene expression / chromatin / 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
heptyl beta-D-glucopyranoside / Chem-D32 / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Z. / Sudom, A. / Walker, N.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Identification of a PPARdelta agonist with partial agonistic activity on PPARgamma.
Authors: Connors, R.V. / Wang, Z. / Harrison, M. / Zhang, A. / Wanska, M. / Hiscock, S. / Fox, B. / Dore, M. / Labelle, M. / Sudom, A. / Johnstone, S. / Liu, J. / Walker, N.P. / Chai, A. / Siegler, K. ...Authors: Connors, R.V. / Wang, Z. / Harrison, M. / Zhang, A. / Wanska, M. / Hiscock, S. / Fox, B. / Dore, M. / Labelle, M. / Sudom, A. / Johnstone, S. / Liu, J. / Walker, N.P. / Chai, A. / Siegler, K. / Li, Y. / Coward, P.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._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 1.3Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,4883
Polymers30,6931
Non-polymers7952
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.577, 92.129, 39.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 30692.668 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain (residues 207-475) / Mutation: G307S, L333I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03181
#2: 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.: 1 / Source method: obtained synthetically / Formula: C13H26O6
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-D32 / (2,3-dimethyl-4-{[2-(prop-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}phenoxy)acetic acid


Mass: 516.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H23F3O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 15% PEG 8000, 0.2 M KCl, 1 mM EDTA, 25% propanediol, 0.5% heptanetriol, 1 mM DTT, 0.1 M Hepes, pH 7.5, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.541 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2004 / Details: 3X3 CCD ARRAY
RadiationMonochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2→94.577 Å / Num. all: 24154 / Num. obs: 24127 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 23.917 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6.225
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.115.30.3721826034340.3799.5
2.11-2.245.60.3042.51834532810.30499.8
2.24-2.395.60.2363.21729430880.23699.9
2.39-2.585.60.18841620228920.188100
2.58-2.835.70.1395.41531126710.139100
2.83-3.165.80.0997.31411524220.099100
3.16-3.655.80.0689.81270321760.068100
3.65-4.475.70.05511.21053918510.055100
4.47-6.325.40.05111.5793214590.051100
6.32-30.334.80.059.841348530.0598.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→94.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.854 / SU B: 4.73 / SU ML: 0.128 / SU R Cruickshank DPI: 0.16 / SU Rfree: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.16 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1233 5.1 %RANDOM
Rwork0.189 ---
obs0.192 24127 99.74 %-
all-24154 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.28 Å2 / Biso mean: 31.825 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--2.71 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2→94.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 55 172 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222216
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.9952991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36524.02197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79115399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1541512
X-RAY DIFFRACTIONr_chiral_restr0.1390.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211618
X-RAY DIFFRACTIONr_mcbond_it1.3961.51308
X-RAY DIFFRACTIONr_mcangle_it2.35422117
X-RAY DIFFRACTIONr_scbond_it3.6393908
X-RAY DIFFRACTIONr_scangle_it5.4184.5874
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 85 -
Rwork0.267 1659 -
all-1744 -
obs--99.03 %

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