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- PDB-5u41: Human PPARdelta ligand-binding domain in complexed with specific ... -

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Basic information

Entry
Database: PDB / ID: 5u41
TitleHuman PPARdelta ligand-binding domain in complexed with specific agonist 16
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 / D-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 / D-glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / negative regulation of myoblast differentiation / Carnitine shuttle / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / fatty acid beta-oxidation / cell-substrate adhesion / negative regulation of cholesterol storage / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / adipose tissue development / cellular response to nutrient levels / fatty acid transport / energy homeostasis / embryo implantation / cholesterol metabolic process / hormone-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / apoptotic signaling pathway / generation of precursor metabolites and energy / fatty acid metabolic process / wound healing / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / nuclear receptor activity / negative regulation of epithelial cell proliferation / glucose metabolic process / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / lipid binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / 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. ...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-7UG / 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: 1.9 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 1.3Nov 22, 2017Group: Refinement description / Category: software
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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)64,68616
Polymers62,2282
Non-polymers2,45814
Water3,189177
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2519
Polymers31,1141
Non-polymers1,1368
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)32,4367
Polymers31,1141
Non-polymers1,3226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.449, 95.124, 95.795
Angle α, β, γ (deg.)90.00, 96.44, 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
#5: 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 , 5 types, 189 molecules

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


Mass: 513.647 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H31NO4S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.87 Å3/Da / Density % sol: 57.14 %
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 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→95.13 Å / Num. obs: 47329 / % possible obs: 85.5 % / Redundancy: 3.2 % / CC1/2: 0.984 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.547 / % possible all: 35.9

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Processing

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

1gwz


Resolution: 1.9→47.595 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1699 3.6 %
Rwork0.2097 --
obs0.2117 47227 85.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→47.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 168 177 4552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064516
X-RAY DIFFRACTIONf_angle_d0.726079
X-RAY DIFFRACTIONf_dihedral_angle_d10.6652719
X-RAY DIFFRACTIONf_chiral_restr0.038690
X-RAY DIFFRACTIONf_plane_restr0.003758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95590.3764720.37671629X-RAY DIFFRACTION37
1.9559-2.01910.4023510.30622061X-RAY DIFFRACTION46
2.0191-2.09120.30571090.29282614X-RAY DIFFRACTION59
2.0912-2.17490.28641880.25014069X-RAY DIFFRACTION92
2.1749-2.27390.3045930.22914318X-RAY DIFFRACTION97
2.2739-2.39380.27961920.2164239X-RAY DIFFRACTION96
2.3938-2.54380.27531970.24034263X-RAY DIFFRACTION97
2.5438-2.74020.2841000.22584507X-RAY DIFFRACTION100
2.7402-3.01590.27321980.22994430X-RAY DIFFRACTION100
3.0159-3.45220.27722000.20734383X-RAY DIFFRACTION100
3.4522-4.34890.23941000.16974548X-RAY DIFFRACTION100
4.3489-47.60990.23871990.1834467X-RAY DIFFRACTION100
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)
10.8937-0.1132-0.06730.79210.4572.58570.0170.020.0431-0.0530.0257-0.0471-0.1559-0.1774-0.0170.18520.03170.00250.15020.01020.1549-7.579-0.064219.762
21.21420.0162-0.22131.02170.05681.5504-0.00390.0466-0.08230.0216-0.0491-0.03530.0517-0.07330.00290.0647-0.02540.00030.0989-0.01240.1227-6.835-37.795208.114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 174:439 )A174 - 439
2X-RAY DIFFRACTION2( CHAIN B AND RESID 173:439 )B173 - 439

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