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- PDB-5u3x: Human PPARdelta ligand-binding domain in complexed with specific ... -

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Basic information

Entry
Database: PDB / ID: 5u3x
TitleHuman PPARdelta ligand-binding domain in complexed with specific agonist 8
ComponentsPeroxisome proliferator-activated receptor delta
Keywordsprotein binding/activator / PPARdelta / ligand-binding domain / agonist / protein binding-activator 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 / 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 / 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 / fatty acid transport / positive regulation of fat cell differentiation / adipose tissue development / energy homeostasis / embryo implantation / hormone-mediated signaling pathway / cholesterol metabolic process / negative regulation of miRNA transcription / fatty acid metabolic process / 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 / 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 / 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 / apoptotic process / lipid binding / 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-7U4 / heptyl beta-D-glucopyranoside / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWu, C.-C. / Baiga, T.J. / Downes, M. / La Clair, J.J. / Atkins, A.R. / Richard, S.B. / Stockley-Noel, T.A. / Bowman, M.E. / Evans, R.M. / Noel, J.P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis for specific ligation of the peroxisome proliferator-activated receptor delta.
Authors: Wu, C.C. / Baiga, T.J. / Downes, M. / La Clair, J.J. / Atkins, A.R. / Richard, S.B. / Fan, W. / Stockley-Noel, T.A. / Bowman, M.E. / Noel, J.P. / Evans, R.M.
History
DepositionDec 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
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 2.1Oct 4, 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)64,40114
Polymers62,2282
Non-polymers2,17312
Water2,090116
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1096
Polymers31,1141
Non-polymers9955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2928
Polymers31,1141
Non-polymers1,1777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.100, 92.940, 96.160
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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: 31114.178 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 131-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03181
#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

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Non-polymers , 4 types, 126 molecules

#2: Chemical ChemComp-7U4 / 6-[2-({cyclopropyl[4-(pyridin-3-yl)benzene-1-carbonyl]amino}methyl)phenoxy]hexanoic acid


Mass: 458.549 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30N2O4
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Bis-tris propane, potassium chloride, PEG 8000, 1,2-propandiol, EDTA, DTT
PH range: 7.5 - 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→92.94 Å / Num. obs: 57201 / % possible obs: 90.8 % / Redundancy: 3.5 % / CC1/2: 0.984 / Net I/σ(I): 4.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 2208 / CC1/2: 0.509 / % possible all: 70.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GWZ

1gwz


Resolution: 2.1→47.609 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 1230 3.15 %
Rwork0.2169 --
obs0.2186 39028 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 152 116 4405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094438
X-RAY DIFFRACTIONf_angle_d1.0255981
X-RAY DIFFRACTIONf_dihedral_angle_d12.8762653
X-RAY DIFFRACTIONf_chiral_restr0.054683
X-RAY DIFFRACTIONf_plane_restr0.006743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.38381250.30953989X-RAY DIFFRACTION94
2.1841-2.28350.37021320.26844215X-RAY DIFFRACTION99
2.2835-2.40390.33531300.24324234X-RAY DIFFRACTION99
2.4039-2.55450.31241500.23234178X-RAY DIFFRACTION99
2.5545-2.75170.29421270.22464244X-RAY DIFFRACTION99
2.7517-3.02860.24471520.22284213X-RAY DIFFRACTION99
3.0286-3.46670.25851150.21514250X-RAY DIFFRACTION99
3.4667-4.36720.24151830.18534219X-RAY DIFFRACTION99
4.3672-47.62080.25831160.20034256X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32930.0578-0.0420.57130.30591.0256-0.1178-0.2127-0.28950.48490.397-0.34580.34640.72320.8045-0.03780.10510.04950.36230.21070.2155-6.1697-0.12133.9302
20.8737-0.45560.22020.9668-0.07771.1865-0.01-0.0383-0.1352-0.1419-0.0319-0.00590.04090.09320.08110.07080.0140.00520.05740.02390.1262-17.12943.6491123.1116
30.0180.0240.04980.36690.12830.4164-0.06230.0928-0.0276-0.05710.1107-0.4436-0.19130.63670.02740.15-0.0738-0.01130.52440.01160.2227-0.578542.2894119.9083
40.1825-0.0169-0.00550.169-0.01260.00230.0877-0.2072-0.0157-0.1566-0.0252-0.0537-0.16070.28470.08150.3886-0.18130.00990.36230.09070.2591-7.094347.221391.7015
51.01070.258-0.53540.7090.00431.23670.03550.010.12330.00070.00360.0557-0.0740.17090.09450.1325-0.0295-0.01710.04480.01580.0848-15.850340.7283115.025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 173:228 )A173 - 228
2X-RAY DIFFRACTION2( CHAIN A AND RESID 234:439 )A234 - 439
3X-RAY DIFFRACTION3( CHAIN B AND RESID 174:203 )B174 - 203
4X-RAY DIFFRACTION4( CHAIN B AND RESID 209:226 )B209 - 226
5X-RAY DIFFRACTION5( CHAIN B AND RESID 235:438 )B235 - 438

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