PDB-2qmv: High Resolution Structure of Peroxisone Proliferation-Activated R...

Basic information

• Entry: Database: PDB / ID: 2qmv
• Title: High Resolution Structure of Peroxisone Proliferation-Activated Receptor gamma and Characterisation of its Interaction with the Co-activator Transcriptional Intermediary Factor 2
• Components: Peroxisome proliferator-activated receptor gamma
• Keywords: transcription regulator / Peroxisome Profileration Activated Receptor gamma / Pparg / Transcriptional Intermediary Factor 2 (TIF2) / Protein Structure / Activator / Diabetes mellitus / Disease mutation / DNA-binding / Metal-binding / Nucleus / Obesity / Phosphorylation / Transcription regulation / Zinc-finger

Function / homology

Function:

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 / 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 / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / 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 / 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 / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / 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 / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / transcription coregulator binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / lipid metabolic process / regulation of circadian rhythm / PPARA activates gene expression / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / rhythmic process / : / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / nucleic acid binding / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding

Domain/homology:

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

Component:

Peroxisome proliferator-activated receptor gamma

• Biological species: Homo sapiens (human)
• Method: SOLUTION NMR / simulated annealing
• Authors: Hartl, R. / Riepl, H. / Kauschke, S. / Kalbitzer, H.R. / Maurer, T.
• Citation: Journal: To be Published; Title: High Resolution Structure of Peroxisone Proliferation-Activated Receptor gamma and Characterisation of its Interaction with the Co-activator Transcriptional Intermediary Factor 2; Authors: Moras, D. / Gronemeyer, H. / Gaal, V.L. / Scheen, A.J. / Cock, T.-A. / Houten, S.M. / Auwerx, J. / Stumvoll, M. / Haering, H. / Uppenberg, J. / Svensson, C. / Jaki, M. / Bertilsson, G. / Jendeberg, L. / Berkenstam, A.

History

Deposition	Jul 17, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 22, 2012	Group: Database references

Assembly

Deposited unit

A: Peroxisome proliferator-activated receptor gamma

Summary:

• 30.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	30,834	1
Polymers	30,834	1
Non-polymers	0	0
Water	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	9 / 1024	structures with the lowest energy
Representative	Model #1	fewest violations

Components

#1: Protein

A Peroxisome proliferator-activated receptor gamma / / PPAR-gamma

Details:

Mass: 30833.850 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain, residues 235-504 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37231

Experimental details

Experiment

• Experiment: Method: SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Type
1	1	1	3D 15N-separated NOESY
1	2	1	3D 13C-separated NOESY
1	3	1	CNH-NOESY

NMR measurement

NMR spectrometer

Type	Manufacturer	Model	Field strength (MHz)	Spectrometer-ID
Bruker DRX	Bruker	DRX	600	1
Bruker DRX	Bruker	DRX	900	2

Processing

NMR software

Name	Version	Developer	Classification
DYANA	1.5	Guentert P.	structure solution
DYANA	1.5	Guentert P.	refinement

• Refinement: Method: simulated annealing / Software ordinal: 1 ; Details: total of 3017 restraints, 2352 are NOE-derived distance constraints, 439 dihedral angle restraints,226 distance restraints from hydrogen bonds.
• NMR representative: Selection criteria: fewest violations
• NMR ensemble: Conformer selection criteria: structures with the lowest energy; Conformers calculated total number: 1024 / Conformers submitted total number: 9