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- PDB-5u40: Human PPARdelta ligand-binding domain in complexed with specific ... -

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Basic information

Entry
Database: PDB / ID: 5u40
TitleHuman PPARdelta ligand-binding domain in complexed with specific agonist 15
ComponentsPeroxisome proliferator-activated receptor delta
Keywordsprotein binding/activator / PPARdelta / ligand-binding domain / agonist / protein binding-activator complex
Function / homology
Function and homology information


keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / positive regulation of epidermis development / axon ensheathment / positive regulation of fat cell proliferation / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration ...keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / positive regulation of epidermis development / axon ensheathment / positive regulation of fat cell proliferation / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration / proteoglycan metabolic process / fatty acid catabolic process / negative regulation of collagen biosynthetic process / positive regulation of myoblast proliferation / 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 / fatty acid beta-oxidation / cell-substrate adhesion / negative regulation of cholesterol storage / decidualization / nuclear steroid receptor activity / keratinocyte proliferation / NF-kappaB binding / adipose tissue development / positive regulation of fat cell differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / response to glucose / fatty acid transport / cellular response to nutrient levels / cholesterol metabolic process / energy homeostasis / intracellular receptor signaling pathway / hormone-mediated signaling pathway / embryo implantation / negative regulation of miRNA transcription / response to activity / generation of precursor metabolites and energy / apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / fatty acid metabolic process / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / vasodilation / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / heart development / cellular response to lipopolysaccharide / cellular response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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-7UD / 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 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)64,58515
Polymers62,2282
Non-polymers2,35713
Water3,279182
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3618
Polymers31,1141
Non-polymers1,2467
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)32,2257
Polymers31,1141
Non-polymers1,1106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.340, 94.750, 95.790
Angle α, β, γ (deg.)90.00, 97.11, 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: 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
#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 , 4 types, 193 molecules

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


Mass: 497.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H31NO5
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
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: 2→95.05 Å / Num. obs: 43342 / % possible obs: 91.9 % / Redundancy: 3 % / CC1/2: 0.975 / Net I/σ(I): 30.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1 / CC1/2: 0.278 / % possible all: 61.5

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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: 2→95.05 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.2295 1864 4.31 %
Rwork0.1926 --
obs0.1942 43257 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→95.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 165 182 4511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034522
X-RAY DIFFRACTIONf_angle_d0.7366091
X-RAY DIFFRACTIONf_dihedral_angle_d12.391675
X-RAY DIFFRACTIONf_chiral_restr0.027690
X-RAY DIFFRACTIONf_plane_restr0.002757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.3551930.33292113X-RAY DIFFRACTION61
2.0541-2.11460.3524910.29482083X-RAY DIFFRACTION61
2.1146-2.18280.38241280.27412706X-RAY DIFFRACTION78
2.1828-2.26080.3011550.24283377X-RAY DIFFRACTION99
2.2608-2.35140.30661460.21443441X-RAY DIFFRACTION99
2.3514-2.45840.26471690.21123438X-RAY DIFFRACTION99
2.4584-2.5880.21711450.19993414X-RAY DIFFRACTION99
2.588-2.75020.23361500.18973427X-RAY DIFFRACTION99
2.7502-2.96250.2451540.1813445X-RAY DIFFRACTION100
2.9625-3.26070.22011550.18153489X-RAY DIFFRACTION100
3.2607-3.73250.17211670.15493449X-RAY DIFFRACTION100
3.7325-4.70260.16151280.14093514X-RAY DIFFRACTION100
4.7026-95.16120.19161830.18373497X-RAY DIFFRACTION99
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)
11.1247-0.17170.11290.97240.23462.21660.02050.02180.066-0.0290.0078-0.0379-0.1143-0.2281-0.0130.12080.02740.00020.13210.01010.098829.12410.2142219.1495
21.62260.3091-0.38991.1503-0.30071.7885-0.05050.1562-0.09440.00210.0046-0.02240.0989-0.2151-0.02490.0317-0.0434-0.00210.1475-0.01990.082229.3943-38.298207.3506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 174:438 OR RESID 501:506 ) ) OR ( CHAIN B AND RESID 501:501 )A174 - 438
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 174:438 OR RESID 501:506 ) ) OR ( CHAIN B AND RESID 501:501 )A501 - 506
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 174:438 OR RESID 501:506 ) ) OR ( CHAIN B AND RESID 501:501 )B501
4X-RAY DIFFRACTION2( CHAIN A AND RESID 507:507 ) OR ( CHAIN B AND ( RESID 174:438 OR RESID 502:506 ) )A507
5X-RAY DIFFRACTION2( CHAIN A AND RESID 507:507 ) OR ( CHAIN B AND ( RESID 174:438 OR RESID 502:506 ) )B174 - 438
6X-RAY DIFFRACTION2( CHAIN A AND RESID 507:507 ) OR ( CHAIN B AND ( RESID 174:438 OR RESID 502:506 ) )B502 - 506

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