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- PDB-6onj: Crystal structure of PPARgamma ligand binding domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 6onj
TitleCrystal structure of PPARgamma ligand binding domain in complex with TRAP220 peptide and agonist rosiglitazone
Components
  • Mediator of RNA polymerase II transcription subunit 1, TRAP220 Coactivator Peptide
  • Peroxisome proliferator-activated receptor gamma
Keywordstranscription/agonist / Nuclear receptors / TZDs / Drug design / Therapeutic targets / TRANSCRIPTION / transcription-agonist complex
Function / homology
Function and homology information


enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / core mediator complex ...enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / prostaglandin receptor activity / cellular response to thyroid hormone stimulus / negative regulation of receptor signaling pathway via STAT / positive regulation of hepatocyte proliferation / MECP2 regulates transcription factors / nuclear vitamin D receptor binding / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / embryonic hindlimb morphogenesis / negative regulation of connective tissue replacement involved in inflammatory response wound healing / nuclear thyroid hormone receptor binding / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding / lens development in camera-type eye / positive regulation of adiponectin secretion / embryonic hemopoiesis / 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 / megakaryocyte development / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / response to lipid / negative regulation of SMAD protein signal transduction / histone acetyltransferase binding / negative regulation of type II interferon-mediated signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / negative regulation of cholesterol storage / RSV-host interactions / lipid homeostasis / fat cell differentiation / E-box binding / alpha-actinin binding / mammary gland branching involved in pregnancy / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / 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 / negative regulation of BMP signaling pathway / general transcription initiation factor binding / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of neuron differentiation / negative regulation of osteoblast differentiation / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / negative regulation of keratinocyte proliferation / positive regulation of fat cell differentiation / ubiquitin ligase complex / negative regulation of MAPK cascade / BMP signaling pathway / nuclear receptor-mediated steroid hormone signaling pathway / embryonic placenta development / animal organ regeneration / long-chain fatty acid transport / erythrocyte development / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha
Similarity search - Function
: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor ...: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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-BRL / Peroxisome proliferator-activated receptor gamma / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsShang, J. / Kojetin, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK101871 United States
CitationJournal: Nat Commun / Year: 2020
Title: A molecular switch regulating transcriptional repression and activation of PPAR gamma.
Authors: Shang, J. / Mosure, S.A. / Zheng, J. / Brust, R. / Bass, J. / Nichols, A. / Solt, L.A. / Griffin, P.R. / Kojetin, D.J.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
C: Mediator of RNA polymerase II transcription subunit 1, TRAP220 Coactivator Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0043
Polymers33,6472
Non-polymers3571
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-13 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.386, 85.574, 121.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-695-

HOH

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 31449.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET46 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1, TRAP220 Coactivator Peptide / Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome ...Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TRIP-2 / Vitamin D receptor-interacting protein complex component DRIP205 / p53 regulatory protein RB18A


Mass: 2197.513 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2
Plasmid: pET46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15648
#3: Chemical ChemComp-BRL / 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) / BRL49653 / ROSIGLITAZONE


Mass: 357.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate trihydrate 0.1M Tris, pH 8.5 30% w/v, PEG 4000

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→36.64 Å / Num. obs: 12926 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 22.96 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 16.54
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.37 / Num. unique obs: 1260 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRG

1prg


Resolution: 2.3→36.64 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.27
RfactorNum. reflection% reflection
Rfree0.273 1290 9.99 %
Rwork0.212 11629 -
obs0.218 12919 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.18 Å2 / Biso mean: 31.11 Å2 / Biso min: 8.51 Å2
Refinement stepCycle: final / Resolution: 2.3→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 25 104 2314
Biso mean--24.65 30.45 -
Num. residues----272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.39210.3271490.24961248100
2.3921-2.5010.29491350.2379126399
2.501-2.63280.34051320.24861291100
2.6328-2.79770.29731400.23711277100
2.7977-3.01360.28391510.24041272100
3.0136-3.31670.33961450.23471282100
3.3167-3.79620.22791440.20171295100
3.7962-4.78110.23811400.17541330100
4.7811-36.640.23871540.1882137199

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