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- PDB-5ycn: Human PPARgamma ligand binding domain complexed with Lobeglitazone -

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Basic information

Entry
Database: PDB / ID: 5ycn
TitleHuman PPARgamma ligand binding domain complexed with Lobeglitazone
Components
  • Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPARgamma / agonist
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / positive regulation of female receptivity / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / positive regulation of female receptivity / 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 / hypothalamus development / STAT family protein binding / male mating behavior / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / estrous cycle / negative regulation of BMP signaling pathway / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / negative regulation of mitochondrial fission / Synthesis of bile acids and bile salts / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / long-chain fatty acid transport / nuclear retinoid X receptor binding / response to retinoic acid / negative regulation of signaling receptor activity / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cell maturation / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / negative regulation of angiogenesis / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / fatty acid metabolic process / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / placenta development / response to progesterone / negative regulation of MAP kinase activity / Regulation of PTEN gene transcription / transcription coregulator binding / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / negative regulation of smooth muscle cell proliferation / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II
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 / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-8LX / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJang, J.Y. / Han, B.W.
CitationJournal: Sci Rep / Year: 2018
Title: Structural Basis for the Enhanced Anti-Diabetic Efficacy of Lobeglitazone on PPAR gamma.
Authors: Jang, J.Y. / Bae, H. / Lee, Y.J. / Choi, Y.I. / Kim, H.J. / Park, S.B. / Suh, S.W. / Kim, S.W. / Han, B.W.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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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)34,6663
Polymers34,1862
Non-polymers4811
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-8 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.959, 53.168, 54.856
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 / / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1905.186 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 685-700 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-8LX / (5S)-5-[[4-[2-[[6-(4-methoxyphenoxy)pyrimidin-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione / Lobeglitazone / Lobeglitazone


Mass: 480.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N4O5S / Comment: agonist*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M sodium citrate tribasic dihydrate (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / % possible obs: 99.8 % / Redundancy: 4.5 % / Net I/σ(I): 31

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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: 5GTO

5gto


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.152 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22832 1033 4.8 %RANDOM
Rwork0.20772 ---
obs0.20879 20491 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.324 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0 Å20 Å2
2--1.11 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 34 113 2353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192279
X-RAY DIFFRACTIONr_bond_other_d0.0040.022272
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.0073068
X-RAY DIFFRACTIONr_angle_other_deg1.0393.0035237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9125271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18425.149101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9115440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1081510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212494
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02492
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_it2.6214.4221093
X-RAY DIFFRACTIONr_mcbond_other2.624.4191092
X-RAY DIFFRACTIONr_mcangle_it3.9536.6041361
X-RAY DIFFRACTIONr_mcangle_other3.9526.6081362
X-RAY DIFFRACTIONr_scbond_it3.324.781185
X-RAY DIFFRACTIONr_scbond_other3.3184.781186
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3047.0031707
X-RAY DIFFRACTIONr_long_range_B_refined7.36635.2092740
X-RAY DIFFRACTIONr_long_range_B_other7.3435.122712
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 85 -
Rwork0.267 1467 -
obs--100 %

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