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- PDB-7cxf: The ligand-free structure of human PPARgamma LBD C285Y mutant in ... -

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Basic information

Entry
Database: PDB / ID: 7cxf
TitleThe ligand-free structure of human PPARgamma LBD C285Y 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 / 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 / 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
Similarity search - Domain/homology
MALONIC 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, 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)34,3503
Polymers34,2462
Non-polymers1041
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-16 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.730, 51.936, 54.133
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: 32340.381 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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
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: 0.9794 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: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 16225 / % possible obs: 99 % / Redundancy: 5.7 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.21
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 778 / CC1/2: 0.874 / % possible all: 97.9

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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: 2.35→48.313 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.369 / SU ML: 0.173 / Cross valid method: FREE R-VALUE / ESU R: 0.396 / ESU R Free: 0.269
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2693 758 5.078 %
Rwork0.2292 14169 -
all0.231 --
obs-14927 93.375 %
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: 38.006 Å2
Baniso -1Baniso -2Baniso -3
1-0.138 Å20 Å20 Å2
2---0.048 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 7 61 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132338
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172275
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.6393147
X-RAY DIFFRACTIONr_angle_other_deg1.1791.5775295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71123.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21115458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.321510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02448
X-RAY DIFFRACTIONr_nbd_refined0.1990.2546
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22117
X-RAY DIFFRACTIONr_nbtor_refined0.1550.21130
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.215
X-RAY DIFFRACTIONr_nbd_other0.3110.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.23
X-RAY DIFFRACTIONr_mcbond_it3.0573.7821130
X-RAY DIFFRACTIONr_mcbond_other3.0553.7771129
X-RAY DIFFRACTIONr_mcangle_it5.065.651409
X-RAY DIFFRACTIONr_mcangle_other5.065.6551410
X-RAY DIFFRACTIONr_scbond_it3.1864.3241207
X-RAY DIFFRACTIONr_scbond_other3.1824.3171205
X-RAY DIFFRACTIONr_scangle_it5.4286.2851737
X-RAY DIFFRACTIONr_scangle_other5.4246.2851737
X-RAY DIFFRACTIONr_lrange_it8.72445.2072635
X-RAY DIFFRACTIONr_lrange_other8.71445.2162629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.344300.275592X-RAY DIFFRACTION55.7348
2.411-2.4770.259390.289809X-RAY DIFFRACTION73.4835
2.477-2.5480.28530.281921X-RAY DIFFRACTION90.3525
2.548-2.6270.317570.271971X-RAY DIFFRACTION95.8955
2.627-2.7130.283580.266976X-RAY DIFFRACTION98.4762
2.713-2.8070.317390.255940X-RAY DIFFRACTION99.3909
2.807-2.9130.306410.266924X-RAY DIFFRACTION99.1778
2.913-3.0320.23480.246896X-RAY DIFFRACTION99.4731
3.032-3.1660.266370.239854X-RAY DIFFRACTION99.6644
3.166-3.320.277450.236807X-RAY DIFFRACTION99.5327
3.32-3.4980.298510.233775X-RAY DIFFRACTION99.7585
3.498-3.710.265470.206747X-RAY DIFFRACTION99.8742
3.71-3.9640.241490.194690X-RAY DIFFRACTION99.8649
3.964-4.2790.246320.184655X-RAY DIFFRACTION100
4.279-4.6840.269280.182620X-RAY DIFFRACTION100
4.684-5.2320.284250.201561X-RAY DIFFRACTION100
5.232-6.030.197280.249492X-RAY DIFFRACTION100
6.03-7.3590.278260.217427X-RAY DIFFRACTION100
7.359-10.2960.243120.192323X-RAY DIFFRACTION92.2865
10.296-48.3130.283130.338186X-RAY DIFFRACTION85.7759

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