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- PDB-5u44: Human PPARdelta ligand-binding domain in complexed with specific ... -

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Basic information

Entry
Database: PDB / ID: 5u44
TitleHuman PPARdelta ligand-binding domain in complexed with specific agonist 13
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-7SV / heptyl beta-D-glucopyranoside / S-1,2-PROPANEDIOL / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 / 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)63,9649
Polymers62,2282
Non-polymers1,7367
Water1,67593
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2996
Polymers31,1141
Non-polymers1,1845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6663
Polymers31,1141
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.570, 95.410, 96.180
Angle α, β, γ (deg.)90.00, 97.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: Ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 2 / Source method: obtained synthetically / Formula: C13H26O6
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-7SV / 6-(2-{[cyclopropyl(2'-fluoro[1,1'-biphenyl]-4-carbonyl)amino]methyl}phenoxy)hexanoic acid


Mass: 475.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H30FNO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
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: Oct 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→95.32 Å / Num. obs: 31224 / % possible obs: 81 % / Redundancy: 3 % / CC1/2: 0.983 / Net I/σ(I): 21.4
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 0.6 / CC1/2: 0.409 / % possible all: 44.8

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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: 2.15→95.32 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.43
RfactorNum. reflection% reflection
Rfree0.2526 1564 5.02 %
Rwork0.1991 --
obs0.2018 31153 80.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→95.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 123 93 4364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024389
X-RAY DIFFRACTIONf_angle_d0.5325926
X-RAY DIFFRACTIONf_dihedral_angle_d10.982638
X-RAY DIFFRACTIONf_chiral_restr0.035676
X-RAY DIFFRACTIONf_plane_restr0.002741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.21950.3275730.30061522X-RAY DIFFRACTION46
2.2195-2.29880.3252920.28691603X-RAY DIFFRACTION49
2.2988-2.39090.3198860.26041674X-RAY DIFFRACTION51
2.3909-2.49970.31811030.27011833X-RAY DIFFRACTION55
2.4997-2.63150.34671550.27183083X-RAY DIFFRACTION93
2.6315-2.79640.29081720.25113177X-RAY DIFFRACTION96
2.7964-3.01230.32041730.2313338X-RAY DIFFRACTION100
3.0123-3.31550.27921850.21343310X-RAY DIFFRACTION100
3.3155-3.79520.22781610.17993315X-RAY DIFFRACTION100
3.7952-4.78160.20941680.14433364X-RAY DIFFRACTION100
4.7816-95.41750.20681960.17563370X-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)
11.4507-0.1474-0.03631.03660.52154.55570.02660.00140.05230.04210.0115-0.0438-0.0509-0.2165-0.03540.27820.01570.04290.19830.02610.210439.8551-0.8193124.4218
22.01670.1765-0.82791.39720.02733.2513-0.05320.1116-0.0810.0378-0.0510.08370.1075-0.30060.06010.2013-0.02180.03620.175-0.00010.200940.8477-39.8648113.1886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 174:438 OR RESID 501:504 ) )A174 - 438
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 174:438 OR RESID 501:504 ) )A501 - 504
3X-RAY DIFFRACTION2( CHAIN A AND RESID 505:505 ) OR ( CHAIN B AND ( RESID 172:438 OR RESID 501:502 ) )A505
4X-RAY DIFFRACTION2( CHAIN A AND RESID 505:505 ) OR ( CHAIN B AND ( RESID 172:438 OR RESID 501:502 ) )B172 - 438
5X-RAY DIFFRACTION2( CHAIN A AND RESID 505:505 ) OR ( CHAIN B AND ( RESID 172:438 OR RESID 501:502 ) )B501 - 502

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