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- PDB-6d94: Crystal structure of PPAR gamma in complex with Mediator of RNA p... -

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Basic information

Entry
Database: PDB / ID: 6d94
TitleCrystal structure of PPAR gamma in complex with Mediator of RNA polymerase II transcription subunit 1
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Peroxisome proliferator-activated receptor gamma
Keywordsdna binding protein/AGONIST / Nuclear receptor / Transcription factor / Super agonist / Ligand binding domain / Coactivator / MED1 / DNA BINDING PROTEIN / dna binding protein-AGONIST complex
Function / homology
Function and homology information


enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone mediated signaling pathway / core mediator complex ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone mediated signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / positive regulation of hepatocyte proliferation / cellular response to thyroid hormone stimulus / embryonic hindlimb morphogenesis / 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 / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / lens development in camera-type eye / nuclear thyroid hormone receptor binding / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / embryonic hemopoiesis / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / megakaryocyte development / erythrocyte development / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding domain binding / cellular response to hepatocyte growth factor stimulus / STAT family protein binding / positive regulation of fatty acid metabolic process / cellular response to steroid hormone stimulus / response to lipid / negative regulation of SMAD protein signal transduction / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / fat cell differentiation / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / mammary gland branching involved in pregnancy / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / general transcription initiation factor binding / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of neuron differentiation / negative regulation of mitochondrial fission / positive regulation of transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / positive regulation of fat cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / animal organ regeneration / ubiquitin ligase complex / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / negative regulation of signaling receptor activity / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / cell maturation / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression
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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...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 / 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-EDK / 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 / Resolution: 1.9 Å
AuthorsMou, T.C. / Chrisman, I.M. / Hughes, T.S. / Sprang, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R00DK103116 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: A structural mechanism of nuclear receptor biased agonism.
Authors: Nemetchek, M.D. / Chrisman, I.M. / Rayl, M.L. / Voss, A.H. / Hughes, T.S.
History
DepositionApr 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2633
Polymers36,7672
Non-polymers4961
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-10 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.437, 87.623, 121.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-719-

HOH

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Components

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


Mass: 34152.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) gold / References: UniProt: P37231
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1 / 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: 2615.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-EDK / (2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid


Mass: 495.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C30H29N3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPES 25% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 3, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→43.81 Å / Num. obs: 23571 / % possible obs: 99.26 % / Redundancy: 9.8 % / Rrim(I) all: 0.09 / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 7.6 / Num. unique obs: 2313 / Rrim(I) all: 0.56 / % possible all: 98.72

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2975: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TTO

5tto


Resolution: 1.9→43.812 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1688 7.16 %
Rwork0.199 --
obs0.2031 23568 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→43.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 37 131 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112374
X-RAY DIFFRACTIONf_angle_d1.2593196
X-RAY DIFFRACTIONf_dihedral_angle_d6.8351452
X-RAY DIFFRACTIONf_chiral_restr0.064365
X-RAY DIFFRACTIONf_plane_restr0.008405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.9560.40261290.36841787X-RAY DIFFRACTION99
1.956-2.01910.34241170.32341805X-RAY DIFFRACTION99
2.0191-2.09130.37751440.28241802X-RAY DIFFRACTION99
2.0913-2.1750.30641570.25621776X-RAY DIFFRACTION99
2.175-2.2740.29191320.24371798X-RAY DIFFRACTION99
2.274-2.39390.28051490.22111806X-RAY DIFFRACTION99
2.3939-2.54380.28861430.2181807X-RAY DIFFRACTION99
2.5438-2.74020.29961410.21371845X-RAY DIFFRACTION100
2.7402-3.01590.28141490.21191813X-RAY DIFFRACTION100
3.0159-3.45220.25411360.18461846X-RAY DIFFRACTION100
3.4522-4.34870.21481390.14111865X-RAY DIFFRACTION100
4.3487-43.82310.1881520.15461930X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.1812 Å / Origin y: -12.4254 Å / Origin z: 13.693 Å
111213212223313233
T0.1391 Å20.0719 Å2-0.0678 Å2-0.3881 Å2-0.0629 Å2--0.1959 Å2
L2.383 °2-0.4007 °2-0.925 °2-2.808 °21.4757 °2--4.1167 °2
S-0.2297 Å °-0.1992 Å °-0.0517 Å °0.2378 Å °0.4392 Å °-0.2741 Å °-0.0691 Å °0.6927 Å °-0.0527 Å °
Refinement TLS groupSelection details: all

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