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- PDB-1wm0: PPARgamma in complex with a 2-BABA compound -

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Basic information

Entry
Database: PDB / ID: 1wm0
TitlePPARgamma in complex with a 2-BABA compound
Components
  • 14-mer from Nuclear receptor coactivator 2
  • Peroxisome proliferator activated receptor gamma
KeywordsTRANSCRIPTION/SIGNALING PROTEIN / three-layer helical domain / TRANSCRIPTION-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 ...Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / nuclear glucocorticoid receptor binding / Estrogen-dependent gene expression / nuclear retinoic acid receptor binding / prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / positive regulation of female receptivity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / nuclear thyroid hormone receptor binding / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / WW 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 / locomotor rhythm / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / aryl hydrocarbon receptor binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / regulation of lipid metabolic process / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / regulation of glucose metabolic process / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / DNA polymerase binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / cellular response to hormone stimulus / epithelial cell differentiation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / nuclear receptor coactivator activity / Regulation of PTEN gene transcription / transcription coregulator binding / response to progesterone / fatty acid metabolic process / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Peroxisome proliferator-activated receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Peroxisome proliferator-activated receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / : / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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-PLB / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 2 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOstberg, T. / Svensson, S. / Selen, G. / Uppenberg, J. / Thor, M. / Sundbom, M. / Sydow-Backman, M. / Gustavsson, A.L. / Jendeberg, L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A new class of peroxisome proliferator-activated receptor agonists with a novel binding epitope shows antidiabetic effects
Authors: Ostberg, T. / Svensson, S. / Selen, G. / Uppenberg, J. / Thor, M. / Sundbom, M. / Sydow-Backman, M. / Gustavsson, A.L. / Jendeberg, L.
History
DepositionJul 1, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
X: Peroxisome proliferator activated receptor gamma
Y: 14-mer from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3833
Polymers34,9782
Non-polymers4041
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-26 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.166, 66.324, 122.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsPPAR/RXR

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Components

#1: Protein Peroxisome proliferator activated receptor gamma / PPAR-gamma


Mass: 33227.352 Da / Num. of mol.: 1 / Fragment: residues 186-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96J12, UniProt: P37231*PLUS
#2: Protein/peptide 14-mer from Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2 / Glucocorticoid receptor-interacting protein 1 / GRIP-1


Mass: 1751.081 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (Mouse)
References: UniProt: Q61026
#3: Chemical ChemComp-PLB / 2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID / 5-(2-PYRIMIDINYLOXY)-2-BENZOYLAMINOBENZOIC ACID


Mass: 404.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H11Cl2N3O4

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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: 3.3 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→14.7 Å / Num. all: 9721 / Num. obs: 8525 / % possible obs: 87.7 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 3.2 / Rsym value: 0.095 / Net I/σ(I): 13.4
Reflection shellResolution: 2.9→3 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→14.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.877 / SU B: 13.536 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 3.2 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29541 441 4.9 %RANDOM
Rwork0.19088 ---
all0.1954 9721 --
obs0.19548 8525 87.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.429 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 27 0 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222338
X-RAY DIFFRACTIONr_angle_refined_deg2.2821.9973146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3345279
X-RAY DIFFRACTIONr_chiral_restr0.1580.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021706
X-RAY DIFFRACTIONr_nbd_refined0.2720.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3760.24
X-RAY DIFFRACTIONr_mcbond_it1.2241.51407
X-RAY DIFFRACTIONr_mcangle_it2.41322275
X-RAY DIFFRACTIONr_scbond_it3.6083931
X-RAY DIFFRACTIONr_scangle_it6.2764.5871
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 41
Rwork0.223 623

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