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- PDB-1y0s: Crystal structure of PPAR delta complexed with GW2331 -

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Basic information

Entry
Database: PDB / ID: 1y0s
TitleCrystal structure of PPAR delta complexed with GW2331
ComponentsPeroxisome proliferator activated receptor delta
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / PPAR / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
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 / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration / positive regulation of myoblast proliferation / proteoglycan metabolic process / fatty acid catabolic process / negative regulation of collagen biosynthetic process / positive regulation of fatty acid oxidation / phospholipid biosynthetic process / Carnitine shuttle / negative regulation of myoblast differentiation / response to vitamin A / Signaling by Retinoic Acid / positive regulation of fatty acid metabolic process / nuclear steroid receptor activity / fatty acid beta-oxidation / negative regulation of cholesterol storage / cell-substrate adhesion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / adipose tissue development / NF-kappaB binding / cellular response to nutrient levels / fatty acid transport / response to glucose / energy homeostasis / intracellular receptor signaling pathway / hormone-mediated signaling pathway / embryo implantation / cholesterol metabolic process / negative regulation of miRNA transcription / response to activity / fatty acid metabolic process / generation of precursor metabolites and energy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / wound healing / transcription coactivator binding / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / nuclear receptor activity / glucose metabolic process / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / vasodilation / heart development / cellular response to lipopolysaccharide / cellular response to hypoxia / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / lipid binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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, 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 / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-331 / heptyl beta-D-glucopyranoside / IODIDE ION / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTakada, I. / Yu, R.T. / Xu, H.E. / Xu, R.X. / Lambert, M.H. / Montana, V.G. / Kliewer, S.A. / Evans, R.M. / Umesono, K.
CitationJournal: MOL.ENDOCRINOL. / Year: 2000
Title: Alteration of a Single Amino Acid in Peroxisome Proliferator-Activated Receptor-alpha (PPARalpha) Generates a PPAR delta Phenotype
Authors: Takada, I. / Yu, R.T. / Xu, H.E. / Lambert, M.H. / Montana, V.G. / Kliewer, S.A. / Evans, R.M. / Umesono, K.
History
DepositionNov 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.4Aug 23, 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

Downloads & links

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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)65,16217
Polymers62,2282
Non-polymers2,93415
Water2,918162
1
A: Peroxisome proliferator activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,77110
Polymers31,1141
Non-polymers1,6579
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3917
Polymers31,1141
Non-polymers1,2776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.356, 94.523, 96.492
Angle α, β, γ (deg.)90.00, 97.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator activated receptor delta / PPAR-delta / PPAR-beta / Nuclear hormone receptor 1 / NUC1 / NUCI


Mass: 31114.178 Da / Num. of mol.: 2 / Fragment: LBD domain (residues 170-441)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): B21 / References: UniProt: Q03181
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-331 / (2S)-2-(4-[2-(3-[2,4-DIFLUOROPHENYL]-1-HEPTYLUREIDO)ETHYL]PHENOXY)-2-METHYLBUTYRIC ACID / GW2331


Mass: 490.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H36F2N2O4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.5 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 35K, KI, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 7, 1997
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 20426 / Num. obs: 19351 / % possible obs: 94.7 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 16
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1963 / Rsym value: 0.413 / % possible all: 97.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GWX

2gwx


Resolution: 2.65→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1135 -random
Rwork0.21 ---
obs0.21 19351 94.7 %-
all-20462 --
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4101 0 189 162 4452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.464

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