PDB-2vsr: hPPARgamma Ligand binding domain in complex with 9-(S)-HODE

Basic information

• Entry: Database: PDB / ID: 2vsr
• Title: hPPARgamma Ligand binding domain in complex with 9-(S)-HODE
• Components: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
• Keywords: RECEPTOR / TRANSCRIPTION REGULATION / ALTERNATIVE SPLICING / LIGAND BINDING DOMAIN / NUCLEAR RECEPTOR / DIABETES MELLITUS / ZINC-FINGER / DNA-BINDING / POLYMORPHISM / TRANSCRIPTION / ZINC / OBESITY / NUCLEUS / ACTIVATOR / OXIDISED FATTY ACID / TRANSCRIPTION FACTOR / METAL-BINDING / PHOSPHOPROTEIN / DISEASE MUTATION

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 / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / 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 / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / negative regulation of signaling receptor activity / cell maturation / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / 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 / nuclear receptor activity / : / rhythmic process / 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 / nucleic acid binding / cell differentiation / 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 / intracellular membrane-bounded organelle / innate immune response / 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:

(9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid / Peroxisome proliferator-activated receptor gamma

• Biological species: HOMO SAPIENS (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
• Authors: Itoh, T. / Fairall, L. / Schwabe, J.W.R.
• Citation: Journal: Nat.Struct.Mol.Biol. / Year: 2008; Title: Structural Basis for the Activation of Pparg by Oxidised Fatty Acids; Authors: Itoh, T. / Fairall, L. / Amin, K. / Inaba, Y. / Szanto, A. / Balint, B.L. / Nagy, L. / Yamamoto, K. / Schwabe, J.W.R.

History

Deposition	Apr 29, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 19, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jun 6, 2012	Group: Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA

B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA

hetero molecules

Summary:

• 63.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	63,788	5
Polymers	62,899	2
Non-polymers	889	3
Water	2,144	119

1

A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA

hetero molecules

Summary:

• defined by author&software
• 32 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	32,042	3
Polymers	31,450	1
Non-polymers	593	2
Water	18