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- PDB-5gtp: The agonist-free structure of human PPARgamma ligand binding doma... -

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Basic information

Entry
Database: PDB / ID: 5gtp
TitleThe agonist-free structure of human PPARgamma ligand binding domain in the presence of the SRC-1 coactivator peptide
Components
  • Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPARgamma / SRC-1
Function / homology
Function and homology information


labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / positive regulation of fatty acid metabolic process / STAT family protein binding / male mating behavior / response to lipid / negative regulation of type II interferon-mediated signaling pathway / hypothalamus development / LBD domain binding / negative regulation of cholesterol storage / negative regulation of SMAD protein signal transduction / E-box binding / lipid homeostasis / alpha-actinin binding / R-SMAD binding / cellular response to Thyroglobulin triiodothyronine / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / Synthesis of bile acids and bile salts / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / progesterone receptor signaling pathway / negative regulation of lipid storage / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cell fate commitment / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / BMP signaling pathway / long-chain fatty acid transport / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / retinoic acid receptor signaling pathway / cell maturation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of MAPK cascade / intracellular receptor signaling pathway / estrogen receptor signaling pathway / hormone-mediated signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / response to nutrient / epithelial cell differentiation / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / negative regulation of miRNA transcription / cerebellum development / negative regulation of angiogenesis / placenta development / nuclear estrogen receptor binding / nuclear receptor binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / Heme signaling / fatty acid metabolic process
Similarity search - Function
Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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 ...Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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 / Nuclear receptor coactivators bHLH domain / 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 / 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
MYRISTIC ACID / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJang, J.Y. / Suh, S.W.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Structural basis for differential activities of enantiomeric PPAR gamma agonists: Binding of S35 to the alternate site.
Authors: Jang, J.Y. / Koh, M. / Bae, H. / An, D.R. / Im, H.N. / Kim, H.S. / Yoon, J.Y. / Yoon, H.J. / Han, B.W. / Park, S.B. / Suh, S.W.
History
DepositionAug 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 gamma
B: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5064
Polymers34,1862
Non-polymers3202
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-6 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.310, 53.062, 53.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 32280.350 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 223-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P37231
#2: Protein/peptide Nuclear receptor coactivator 1


Mass: 1905.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788*PLUS
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2 M sodium malonate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 16193 / % possible obs: 99.4 % / Redundancy: 5.8 % / Net I/σ(I): 36.2
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VN2

3vn2


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.223 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25809 817 5.1 %RANDOM
Rwork0.21066 ---
obs0.21292 15328 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.958 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å2-0 Å2-0 Å2
2--0.82 Å2-0 Å2
3---1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 22 45 2263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192270
X-RAY DIFFRACTIONr_bond_other_d0.0060.022302
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9923047
X-RAY DIFFRACTIONr_angle_other_deg1.1813.0055311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64824.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.415447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4391512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.826.3741089
X-RAY DIFFRACTIONr_mcbond_other4.8176.371088
X-RAY DIFFRACTIONr_mcangle_it7.1479.531357
X-RAY DIFFRACTIONr_mcangle_other7.1459.5341358
X-RAY DIFFRACTIONr_scbond_it5.2827.1091180
X-RAY DIFFRACTIONr_scbond_other5.2817.1111181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.44910.3661688
X-RAY DIFFRACTIONr_long_range_B_refined11.4550.4092592
X-RAY DIFFRACTIONr_long_range_B_other11.44950.4092592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 61 -
Rwork0.271 1099 -
obs--100 %

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