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- PDB-2znn: Human PPAR alpha ligand binding domain in complex with a syntheti... -

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Basic information

Entry
Database: PDB / ID: 2znn
TitleHuman PPAR alpha ligand binding domain in complex with a synthetic agonist TIPP703
ComponentsPeroxisome proliferator-activated receptor alpha
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / PROTEIN-LIGAND COMPLEX / PPAR / Activator / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger
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 / positive regulation of fatty acid oxidation / regulation of fatty acid metabolic process / cellular response to fructose stimulus / regulation of ketone metabolic process / behavioral response to nicotine / negative regulation of appetite ...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 / positive regulation of fatty acid oxidation / regulation of fatty acid metabolic process / cellular response to fructose stimulus / regulation of ketone metabolic process / behavioral response to nicotine / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / nitric oxide metabolic process / positive regulation of fatty acid metabolic process / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of reactive oxygen species biosynthetic process / negative regulation of signaling receptor activity / MDM2/MDM4 family protein binding / positive regulation of gluconeogenesis / RORA activates gene expression / negative regulation of blood pressure / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cellular response to starvation / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / gluconeogenesis / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / SUMOylation of intracellular receptors / wound healing / response to insulin / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / nuclear receptor activity / Circadian Clock / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / lipid binding / protein-containing complex binding / chromatin / 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 alpha / 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. ...Peroxisome proliferator-activated receptor alpha / 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-S44 / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsOyama, T. / Toyota, K. / Kasuga, J. / Miyachi, H. / Morikawa, K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures
Authors: Oyama, T. / Toyota, K. / Waku, T. / Hirakawa, Y. / Nagasawa, N. / Kasuga, J. / Hashimoto, Y. / Miyachi, H. / Morikawa, K.
#1: Journal: To be Published
Title: Peroxisome proliferator-activated receptor (PPAR) agonists with a 3,4-dihydro-2H-benzo[e][1,3]oxazine and 2,3,4,5-tetrahydrobenzo[f][1,4]oxazepine skeleton: effects of the conformational ...Title: Peroxisome proliferator-activated receptor (PPAR) agonists with a 3,4-dihydro-2H-benzo[e][1,3]oxazine and 2,3,4,5-tetrahydrobenzo[f][1,4]oxazepine skeleton: effects of the conformational restriction on PPAR agonistic acivity
Authors: Ohkane, K. / Kasuga, J. / Oyama, T. / Hirakawa, Y. / Morikawa, K. / Makishima, M. / Hashimoto, Y. / Miyachi, H.
#2: Journal: To be Published
Title: Improvement of the transactivation activity of phenylpropanoic acid-type peroxisome proliferator-acitvated rectpror pan agonists; effect of introduction of fluorine at the linker part
Authors: Kasuga, J. / Oyama, T. / Hirakawa, Y. / Makishima, M. / Morikawa, K. / Hashimoto, Y. / Miyachi, H.
History
DepositionApr 30, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Mar 2, 2016Group: Structure summary
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,3602
Polymers30,8561
Non-polymers5041
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.370, 61.530, 53.120
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30856.053 Da / Num. of mol.: 1 / Fragment: Ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA, NR1C1, PPAR / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q07869
#2: Chemical ChemComp-S44 / (2S)-2-(4-propoxy-3-{[({4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]phenyl}carbonyl)amino]methyl}benzyl)butanoic acid / (S)-2-{3-[(4-adamantan-1-ylbenzoylamino)methyl]-4-propoxybenzyl} butyric acid


Mass: 503.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H41NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 13, 2007
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18142 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.222 / Num. unique all: 1646 / % possible all: 90.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1I7G

1i7g


Resolution: 2.01→35.02 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 114228.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 853 4.8 %RANDOM
Rwork0.214 ---
obs0.214 17589 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8196 Å2 / ksol: 0.380038 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.78 Å20 Å25.46 Å2
2---2.32 Å20 Å2
3----4.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.01→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 37 146 2237
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 134 5.5 %
Rwork0.252 2282 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3703_param.txt703_top.txt

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