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- PDB-5u42: Human PPARdelta ligand-binding domain in complexed with specific ... -

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Basic information

Entry
Database: PDB / ID: 5u42
TitleHuman PPARdelta ligand-binding domain in complexed with specific agonist 11
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 / negative regulation of myoblast differentiation / Carnitine metabolism / 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 / positive regulation of fat cell differentiation / fatty acid transport / adipose tissue development / energy homeostasis / embryo implantation / cholesterol metabolic process / hormone-mediated signaling pathway / fatty acid metabolic process / negative regulation of miRNA transcription / 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-7SM / 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: 1.7 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)64,76715
Polymers62,2282
Non-polymers2,53913
Water6,341352
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8019
Polymers31,1141
Non-polymers1,6878
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)31,9666
Polymers31,1141
Non-polymers8525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.660, 95.130, 96.520
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 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: Ligand-binding domain
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
#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.: 3 / Source method: obtained synthetically / Formula: C13H26O6
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 362 molecules

#3: Chemical ChemComp-7SM / 6-(2-{[cyclopropyl(3'-methoxy[1,1'-biphenyl]-4-carbonyl)amino]methyl}phenoxy)hexanoic acid


Mass: 487.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H33NO5
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / 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: 1.57→95.13 Å / Num. obs: 91316 / % possible obs: 92.5 % / Redundancy: 77.7 % / CC1/2: 0.995 / Net I/σ(I): 61.8
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 1.5 % / CC1/2: 0.497 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX1.9pre_1665refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GWZ

1gwz


Resolution: 1.7→47.786 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.23
RfactorNum. reflection% reflection
Rfree0.2156 1423 2 %
Rwork0.1745 --
obs0.1753 71181 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→47.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 177 352 4825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124721
X-RAY DIFFRACTIONf_angle_d1.4036370
X-RAY DIFFRACTIONf_dihedral_angle_d14.2251767
X-RAY DIFFRACTIONf_chiral_restr0.057718
X-RAY DIFFRACTIONf_plane_restr0.006790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76080.3461910.3564522X-RAY DIFFRACTION59
1.7608-1.83130.34581250.3225991X-RAY DIFFRACTION79
1.8313-1.91460.33491320.276766X-RAY DIFFRACTION89
1.9146-2.01560.27951560.22977152X-RAY DIFFRACTION94
2.0156-2.14180.19481540.18457365X-RAY DIFFRACTION97
2.1418-2.30720.21551470.17267496X-RAY DIFFRACTION98
2.3072-2.53940.19841410.16447524X-RAY DIFFRACTION99
2.5394-2.90680.21761760.16967567X-RAY DIFFRACTION99
2.9068-3.6620.18711120.15987689X-RAY DIFFRACTION100
3.662-47.80440.19181890.13797686X-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)
11.30230.053-0.36581.4596-0.63992.5386-0.0144-0.0835-0.0436-0.0906-0.036-0.05630.03520.16180.02890.08020.0077-0.01090.11450.01340.1443-15.21262.7218125.787
21.11180.1134-0.19631.0058-0.51594.30550.0250.07670.0846-0.08240.0571-0.0131-0.21390.2089-0.06640.1522-0.00050.00830.1476-0.00050.1636-13.396640.6988113.7975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 170:440 OR RESID 501:507 ) )A170 - 440
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 170:440 OR RESID 501:507 ) )A501 - 507
3X-RAY DIFFRACTION2( CHAIN A AND RESID 508:508 ) OR ( CHAIN B AND ( RESID 173:440 OR RESID 501:505 ) )A508
4X-RAY DIFFRACTION2( CHAIN A AND RESID 508:508 ) OR ( CHAIN B AND ( RESID 173:440 OR RESID 501:505 ) )B173 - 440
5X-RAY DIFFRACTION2( CHAIN A AND RESID 508:508 ) OR ( CHAIN B AND ( RESID 173:440 OR RESID 501:505 ) )B501 - 505

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