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- PDB-3e00: Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bou... -

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Basic information

Entry
Database: PDB / ID: 3
TitleIntact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with GW9662, 9-cis Retinoic Acid and NCOA2 Peptide
Components
  • DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3')
  • DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3')
  • NCOA2 Peptide
  • Peroxisome proliferator-activated receptor gamma
  • Retinoic acid receptor RXR-alpha
KeywordsTranscription/DNA / DNA-binding / Host-virus interaction / Metal-binding / Nucleus / Receptor / Transcription / Transcription regulation / Zinc-finger / Activator / Diabetes mellitus / Disease mutation / Obesity / Phosphoprotein / Transcription-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / positive regulation of vitamin D receptor signaling pathway / MECP2 regulates transcription factors / nuclear vitamin D receptor binding / 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 / Signaling by Retinoic Acid / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / response to lipid / 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 / locomotor rhythm / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / aryl hydrocarbon receptor binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / regulation of glucose metabolic process / 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 / positive regulation of bone mineralization / long-chain fatty acid transport / nuclear retinoid X receptor binding / response to retinoic acid / transcription regulator inhibitor activity / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / cell maturation / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / : / 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 / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / peptide binding / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of angiogenesis / transcription coregulator binding / response to progesterone / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / nuclear receptor binding / fatty acid metabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Nuclear receptor coactivator 2 ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(9cis)-retinoic acid / 2-chloro-5-nitro-N-phenylbenzamide / DNA / DNA (> 10) / Retinoic acid receptor RXR-alpha / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChandra, V. / Huang, P. / Hamuro, Y. / Raghuram, S. / Wang, Y. / Burris, T.P. / Rastinejad, F.
CitationJournal: Nature / Year: 2008
Title: Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA.
Authors: Chandra, V. / Huang, P. / Hamuro, Y. / Raghuram, S. / Wang, Y. / Burris, T.P. / Rastinejad, F.
History
DepositionJul 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 16, 2012Group: Database references
Revision 1.3Nov 16, 2016Group: Non-polymer description
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
D: Peroxisome proliferator-activated receptor gamma
C: DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3')
F: DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3')
G: NCOA2 Peptide
E: NCOA2 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,04112
Polymers115,2026
Non-polymers8396
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-61 kcal/mol
Surface area36860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.585, 146.775, 67.230
Angle α, β, γ (deg.)90.000, 115.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Retinoic acid receptor RXR-alpha / Retinoid X receptor alpha / Nuclear receptor subfamily 2 group B member 1


Mass: 51527.863 Da / Num. of mol.: 1 / Fragment: UNP residues 11-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR2B1, RXRA, RXRalpha / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19793
#2: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 48163.645 Da / Num. of mol.: 1 / Fragment: UNP residues 102-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1C3, PPARG, PPARgamma / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231

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DNA chain , 2 types, 2 molecules CF

#3: DNA chain DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3')


Mass: 6176.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#4: DNA chain DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3')


Mass: 6090.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA

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Protein/peptide , 1 types, 2 molecules GE

#5: Protein/peptide NCOA2 Peptide


Mass: 1621.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q15596

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Non-polymers , 3 types, 6 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#8: Chemical ChemComp-GW9 / 2-chloro-5-nitro-N-phenylbenzamide


Mass: 276.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9ClN2O3

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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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-18% PEG 3350, 25mM MgCl2, 100mM NH4Cl, 5mM DTT and 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2MES11
3MgCl212
4MES12
5PEG 335012
6NH4Cl12
7DTT12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 20098 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.097 / Χ2: 1.006
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.486 / Num. unique all: 1843 / Χ2: 0.933 / % possible all: 90.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→46.76 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1823 9.8 %RANDOM
Rwork0.214 ---
obs-18669 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.87 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 88.6 Å2
Baniso -1Baniso -2Baniso -3
1-10.94 Å20 Å214.57 Å2
2--3.22 Å20 Å2
3----14.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.1→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5385 814 45 0 6244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 250 9.8 %
Rwork0.34 2289 -
obs-2539 75.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4rea.par
X-RAY DIFFRACTION5gw9.par

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