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- PDB-6ktn: Human PPARgamma ligand-binding domain R288A mutant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6ktn
TitleHuman PPARgamma ligand-binding domain R288A mutant in complex with imatinib
Components
  • 16-mer peptide from Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Type 2 diabetes mellitus
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 / DNA binding domain binding / lipoprotein transport / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K4 acetyltransferase activity / male mating behavior / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / negative regulation of cholesterol storage / histone H4K16 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K122 acetyltransferase activity / hypothalamus development / lipid homeostasis / E-box binding / histone H3K18 acetyltransferase activity / alpha-actinin binding / histone H3K27 acetyltransferase activity / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of blood vessel endothelial cell migration / monocyte differentiation / 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 / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / cell fate commitment / negative regulation of mitochondrial fission / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / Endogenous sterols / 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 / estrous cycle / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / retinoic acid receptor signaling pathway / cell maturation / Recycling of bile acids and salts / negative regulation of MAPK cascade / histone acetyltransferase / intracellular receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / estrogen receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / : / 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 / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / placenta development
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
Chem-STI / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.752 Å
AuthorsJang, J.Y. / Han, B.W.
CitationJournal: Molecules / Year: 2019
Title: Structural Basis for the Regulation of PPAR gamma Activity by Imatinib.
Authors: Jang, J.Y. / Kim, H.J. / Han, B.W.
History
DepositionAug 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)34,5933
Polymers34,0992
Non-polymers4941
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-16 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.928, 52.779, 53.438
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: 32194.236 Da / Num. of mol.: 1 / Mutation: R316A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / 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-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB


Mass: 493.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31N7O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 10176 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 30.1
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.679 / Num. unique obs: 507 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JQ7

6jq7


Resolution: 2.752→30.002 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.654 / SU ML: 0.238 / Cross valid method: FREE R-VALUE / ESU R: 3.172 / ESU R Free: 0.362
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2563 459 4.742 %
Rwork0.2205 --
all0.222 --
obs-9680 95.482 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.559 Å20 Å20 Å2
2---0.126 Å20 Å2
3----0.433 Å2
Refinement stepCycle: LAST / Resolution: 2.752→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 37 30 2283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132295
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172239
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.6623088
X-RAY DIFFRACTIONr_angle_other_deg1.3441.6065205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65723.853109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70215443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.772159
X-RAY DIFFRACTIONr_chiral_restr0.0540.2297
X-RAY DIFFRACTIONr_chiral_restr_other1.7190.29
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022464
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02446
X-RAY DIFFRACTIONr_nbd_refined0.2090.2584
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.22184
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21150
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.21036
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0240.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.210
X-RAY DIFFRACTIONr_nbd_other0.2030.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3390.22
X-RAY DIFFRACTIONr_mcbond_it3.2094.5231097
X-RAY DIFFRACTIONr_mcbond_other3.2084.521096
X-RAY DIFFRACTIONr_mcangle_it5.3676.7581366
X-RAY DIFFRACTIONr_mcangle_other5.3666.7621367
X-RAY DIFFRACTIONr_scbond_it3.5535.041197
X-RAY DIFFRACTIONr_scbond_other3.5525.0411198
X-RAY DIFFRACTIONr_scangle_it5.877.3631721
X-RAY DIFFRACTIONr_scangle_other5.8697.3641722
X-RAY DIFFRACTIONr_lrange_it9.12854.7212679
X-RAY DIFFRACTIONr_lrange_other9.12654.7172680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.752-2.8220.201190.2194110.2187370.9210.91958.34460.194
2.822-2.8990.288260.2565790.2587030.8890.986.05970.221
2.899-2.9820.296370.2596140.2616880.8360.89494.62210.22
2.982-3.0730.203360.2456250.2436610.9260.9071000.21
3.073-3.1730.217360.2376080.2366480.9270.9299.38270.198
3.173-3.2830.302310.2396180.2426490.8720.9141000.205
3.283-3.4050.377200.2335770.2385970.8680.9061000.201
3.405-3.5420.322200.245760.2435960.8740.9151000.216
3.542-3.6980.274300.2275300.2295600.8960.9281000.202
3.698-3.8750.225260.2065160.2075420.9440.9481000.188
3.875-4.0810.186240.1875080.1875320.9510.9561000.182
4.081-4.3230.238250.1894640.1924890.9430.9561000.184
4.323-4.6150.22300.1924290.1944590.9540.9561000.198
4.615-4.9750.193120.1864320.1864440.9390.9541000.191
4.975-5.4350.303170.2354020.2374190.9190.9421000.244
5.435-6.0520.554180.2923500.3023680.830.9051000.291
6.052-6.9410.261180.2623150.2623330.890.9191000.27
6.941-8.390.23870.1952900.1962970.9410.961000.227
8.39-11.4260.213140.1672220.1692360.9660.9781000.199
11.426-30.0020.243130.3071550.3011680.9590.9311000.383

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