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- PDB-7cxi: The ligand-free structure of human PPARgamma LBD F287Y mutant in ... -

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Basic information

Entry
Database: PDB / ID: 7cxi
TitleThe ligand-free structure of human PPARgamma LBD F287Y mutant in the presence of the SRC-1 coactivator peptide
Components
  • 16-mer peptide from Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor / ligand binding domain / mutant
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 / negative regulation of connective tissue replacement involved in inflammatory response wound healing ...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 / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / response to lipid / male mating behavior / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / Synthesis of bile acids and bile salts / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of fat cell differentiation / Endogenous sterols / negative regulation of MAPK cascade / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / cell maturation / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / estrogen receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / peptide binding / SUMOylation of transcription cofactors
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 / 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
Similarity search - Domain/homology
MALONATE ION / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJang, D.M. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2011-0030001 Korea, Republic Of
CitationJournal: To Be Published
Title: The ligand-free structure of human PPARgamma LBD
Authors: Jang, D.M. / Han, B.W.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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: 16-mer peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3043
Polymers34,2022
Non-polymers1021
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-6 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.748, 52.377, 53.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 32296.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide 16-mer peptide from Nuclear receptor coactivator 1


Mass: 1905.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 295 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17093 / % possible obs: 99.6 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 31.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.06 / Num. unique obs: 839 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GTP

5gtp


Resolution: 2.3→48.668 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.908 / SU ML: 0.184 / Cross valid method: FREE R-VALUE / ESU R: 0.332 / ESU R Free: 0.247
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2761 831 5.037 %
Rwork0.2434 15667 -
all0.245 --
obs-16498 96.221 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.091 Å2
Baniso -1Baniso -2Baniso -3
1-0.283 Å2-0 Å20 Å2
2---0.158 Å2-0 Å2
3----0.124 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 7 26 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132239
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172188
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.6373011
X-RAY DIFFRACTIONr_angle_other_deg1.2081.5795088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92423.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7815441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8221510
X-RAY DIFFRACTIONr_chiral_restr0.060.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined0.2150.2498
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21978
X-RAY DIFFRACTIONr_nbtor_refined0.1560.21086
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3450.29
X-RAY DIFFRACTIONr_nbd_other0.3290.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.250.23
X-RAY DIFFRACTIONr_mcbond_it3.6064.0771085
X-RAY DIFFRACTIONr_mcbond_other3.6074.0731084
X-RAY DIFFRACTIONr_mcangle_it5.8736.0841351
X-RAY DIFFRACTIONr_mcangle_other5.8716.0891352
X-RAY DIFFRACTIONr_scbond_it3.7284.6691153
X-RAY DIFFRACTIONr_scbond_other3.734.6611151
X-RAY DIFFRACTIONr_scangle_it6.5766.7511659
X-RAY DIFFRACTIONr_scangle_other6.5776.7511659
X-RAY DIFFRACTIONr_lrange_it10.03847.4162494
X-RAY DIFFRACTIONr_lrange_other10.04247.4212491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.454490.314842X-RAY DIFFRACTION70.6582
2.36-2.4240.444430.2921004X-RAY DIFFRACTION87.7619
2.424-2.4940.296490.2981085X-RAY DIFFRACTION96.2649
2.494-2.5710.337670.3051074X-RAY DIFFRACTION99.4769
2.571-2.6550.311570.3111042X-RAY DIFFRACTION99.9091
2.655-2.7480.34620.2821027X-RAY DIFFRACTION99.9083
2.748-2.8510.395400.289986X-RAY DIFFRACTION99.9026
2.851-2.9670.334470.298960X-RAY DIFFRACTION100
2.967-3.0990.24480.288912X-RAY DIFFRACTION100
3.099-3.2490.364320.25895X-RAY DIFFRACTION100
3.249-3.4240.265520.245832X-RAY DIFFRACTION100
3.424-3.6310.227530.22787X-RAY DIFFRACTION100
3.631-3.880.244580.221725X-RAY DIFFRACTION100
3.88-4.1890.208340.188716X-RAY DIFFRACTION100
4.189-4.5850.212330.185648X-RAY DIFFRACTION100
4.585-5.1210.261220.18604X-RAY DIFFRACTION100
5.121-5.9030.207330.225536X-RAY DIFFRACTION100
5.903-7.2050.312240.217454X-RAY DIFFRACTION100
7.205-10.0850.206140.176349X-RAY DIFFRACTION92.3664
10.085-48.6680.249140.332188X-RAY DIFFRACTION81.7814

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