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- PDB-4ci5: Structural basis for GL479 a dual Peroxisome Proliferator-Activat... -

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Basic information

Entry
Database: PDB / ID: 4ci5
TitleStructural basis for GL479 a dual Peroxisome Proliferator-Activated Receptor gamma agonist
ComponentsPEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
KeywordsNUCLEAR PROTEIN / DUAL AGONIST / NUCLEAR RECEPTOR
Function / homology
Function and homology information


prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding ...prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / DNA binding domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / placenta development / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / cellular response to insulin stimulus / RNA polymerase II transcription regulator complex / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear receptor activity / : / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / 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 gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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) ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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-Y1N / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSantos, J.C. / Bernardes, A. / Polikarpov, I.
CitationJournal: J. Struct. Biol. / Year: 2015
Title: Different binding and recognition modes of GL479, a dual agonist of Peroxisome Proliferator-Activated Receptor alpha / gamma.
Authors: dos Santos, J.C. / Bernardes, A. / Giampietro, L. / Ammazzalorso, A. / De Filippis, B. / Amoroso, R. / Polikarpov, I.
History
DepositionDec 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9974
Polymers62,1882
Non-polymers8092
Water8,881493
1
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4992
Polymers31,0941
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4992
Polymers31,0941
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.488, 64.247, 118.781
Angle α, β, γ (deg.)90.00, 102.59, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 207:239)
211CHAIN B AND (RESSEQ 207:239)
311CHAIN B AND (RESSEQ 245:262)
411CHAIN B AND (RESSEQ 276:282)

NCS oper: (Code: given
Matrix: (0.0776, 0.9874, 0.138), (0.9833, -0.0987, 0.153), (0.1647, 0.1238, -0.9786)
Vector: 31.5011, -36.4358, 48.4776)

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Components

#1: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA / / PPAR-GAMMA / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3


Mass: 31094.135 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 206-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-Y1N / 2-methyl-2-[4-[2-[4-[(E)-phenyldiazenyl]phenoxy]ethyl]phenoxy]propanoic acid


Mass: 404.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24N2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.66 Å3/Da / Density % sol: 53.74 % / Description: NONE
Crystal growDetails: 0.8 M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1 M HEPES PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.77→37.85 Å / Num. obs: 62608 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 23.28 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SZ1

3sz1


Resolution: 1.77→32.535 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 3174 5.1 %
Rwork0.1754 --
obs0.1773 62598 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→32.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 60 493 4643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074272
X-RAY DIFFRACTIONf_angle_d1.0885785
X-RAY DIFFRACTIONf_dihedral_angle_d14.9051603
X-RAY DIFFRACTIONf_chiral_restr0.073672
X-RAY DIFFRACTIONf_plane_restr0.005734
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13BX-RAY DIFFRACTIONPOSITIONAL
14BX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.79640.31091190.24922522X-RAY DIFFRACTION98
1.7964-1.82450.27821310.24142597X-RAY DIFFRACTION98
1.8245-1.85440.2441400.23132488X-RAY DIFFRACTION98
1.8544-1.88640.27571280.22952606X-RAY DIFFRACTION98
1.8864-1.92070.23991400.21592510X-RAY DIFFRACTION98
1.9207-1.95760.28341240.21492619X-RAY DIFFRACTION98
1.9576-1.99760.23321430.19982531X-RAY DIFFRACTION98
1.9976-2.0410.26081380.18842552X-RAY DIFFRACTION98
2.041-2.08850.21471280.18482597X-RAY DIFFRACTION99
2.0885-2.14070.22281470.17862583X-RAY DIFFRACTION99
2.1407-2.19860.231310.16832580X-RAY DIFFRACTION99
2.1986-2.26320.20931350.1792595X-RAY DIFFRACTION99
2.2632-2.33630.2271300.17362594X-RAY DIFFRACTION99
2.3363-2.41970.22661340.17112567X-RAY DIFFRACTION99
2.4197-2.51660.22431380.16962624X-RAY DIFFRACTION99
2.5166-2.63110.18891460.17722586X-RAY DIFFRACTION99
2.6311-2.76970.22691430.17652611X-RAY DIFFRACTION99
2.7697-2.94310.2071540.17752575X-RAY DIFFRACTION99
2.9431-3.17020.22411490.17962592X-RAY DIFFRACTION99
3.1702-3.48890.21571460.16952594X-RAY DIFFRACTION99
3.4889-3.9930.17641610.15132605X-RAY DIFFRACTION99
3.993-5.02780.18481460.14862639X-RAY DIFFRACTION99
5.0278-32.54050.20211230.18052657X-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)
12.65420.06740.15176.2382-1.43122.34330.1089-0.1349-0.20390.0158-0.04670.35560.1376-0.2618-0.06610.1863-0.0189-0.02830.2476-0.00060.243-3.6954-11.163720.0357
21.7860.8275-0.7371.1896-1.13321.0763-0.09290.4921-0.0055-0.2260.21240.0294-0.0337-0.2293-0.10540.24760.001-0.00670.2948-0.01290.23028.48730.26860.9331
31.6117-0.2771-0.71023.55911.33252.5706-0.0860.34110.76660.22580.0467-0.0767-0.905-0.16250.06850.6386-0.06760.06530.40140.10810.562719.542915.5264-0.7818
45.89023.2435-3.15582.9933-1.89572.4094-0.02350.29230.6305-0.20870.21110.1917-0.2998-0.0057-0.13990.3441-0.0462-0.03240.27660.02380.29312.32768.824917.0766
51.1792-0.4414-0.75160.44410.18882.07840.031-0.21770.1390.08960.0399-0.0661-0.19190.2005-0.05430.2296-0.0139-0.02520.2216-0.00320.20979.2264-1.265827.4661
61.46340.4492-0.12561.6983-0.5562.4708-0.0407-0.035-0.01060.041-0.0404-0.2917-0.14610.36850.08760.2555-0.0124-0.00560.275-0.0140.250721.47911.06127.5781
71.18790.10890.39350.92280.14563.34040.0294-0.0487-0.13780.07370.0521-0.08020.11340.16230.01430.22930.0021-0.01750.23320.01040.23499.2244-8.679223.8194
82.2750.30240.71172.7750.46132.66410.0937-0.0163-0.50870.03950.1603-0.20670.39940.0038-0.12780.2169-0.0076-0.00970.20530.02430.31025.0536-17.406323.8039
93.12754.50550.52927.30820.84020.10490.1024-0.1196-0.48690.1775-0.0569-0.91750.05560.2306-0.03980.26240.0065-0.03730.33050.04770.345422.3382-4.371221.5857
104.19062.0576-1.06743.04410.33940.64250.1675-0.17160.25160.56870.1063-0.0103-0.06430.3343-0.19190.335-0.0567-0.01970.297-0.03940.321820.098812.618825.5763
114.15230.74450.94232.41541.04722.85490.0339-0.2105-0.37390.03750.03850.03960.3014-0.1669-0.04940.2942-0.03420.01360.22510.04010.318117.4039-40.427927.1511
121.78080.98591.05712.6372-0.49695.77680.1319-0.82820.01380.4778-0.1426-0.08150.46750.1289-0.10560.39850.011-0.00920.37150.08170.291624.3719-33.252343.5563
132.5456-0.5822-1.00261.47340.69553.6801-0.06-0.9205-0.17270.31690.06910.04950.13720.4731-0.0690.44660.02010.02560.62140.03360.286340.4584-25.576951.8283
141.410.01740.14220.51970.06721.5926-0.017-0.25020.05310.1320.02940.0343-0.19050.05640.00250.26870.00910.00860.23220.01780.232729.5908-24.782934.9923
152.30990.3002-0.73841.1541-0.51252.34550.03410.1438-0.0086-0.06680.06640.28480.0111-0.2507-0.05690.22220.0141-0.02230.21090.00330.266116.2798-28.97420.9473
163.8039-0.05210.54420.19150.15860.09-0.06860.15890.7592-0.06030.0551-0.0083-0.17960.09020.04640.39230.00050.01240.3280.01740.384134.3219-16.799830.538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 206 THROUGH 225 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 226 THROUGH 251 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 252 THROUGH 276 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 277 THROUGH 302 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 303 THROUGH 333 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 334 THROUGH 377 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 378 THROUGH 402 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 403 THROUGH 430 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 431 THROUGH 459 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 460 THROUGH 477 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 207 THROUGH 225 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 226 THROUGH 238 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 239 THROUGH 276 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 277 THROUGH 392 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 393 THROUGH 430 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 431 THROUGH 477 )

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