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- PDB-2prg: LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVA... -

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Basic information

Entry
Database: PDB / ID: 2prg
TitleLIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
Components
  • NUCLEAR RECEPTOR COACTIVATOR SRC-1
  • PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
KeywordsCOMPLEX (THIAZOLIDINEDIONE/RECEPTOR) / COMPLEX (THIAZOLIDINEDIONE-RECEPTOR) / LIGAND-BINDING DOMAIN / NUCLEAR RECEPTOR / APO / TRANSCRIPTION FACTOR / ORPHAN RECEPTOR / COMPLEX (THIAZOLIDINEDIONE-RECEPTOR) complex
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / positive regulation of female receptivity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / positive regulation of female receptivity / 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 / hypothalamus development / male mating behavior / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / estrous cycle / 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 / cellular response to Thyroglobulin triiodothyronine / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / Synthesis of bile acids and bile salts / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / negative regulation of signaling receptor activity / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cell maturation / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / fatty acid metabolic process / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / response to progesterone / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / nuclear estrogen receptor binding / transcription coregulator binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II
Similarity search - Function
Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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 ...Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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 / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-BRL / Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNolte, R.T. / Wisely, G.B. / Milburn, M.V.
CitationJournal: Nature / Year: 1998
Title: Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma.
Authors: Nolte, R.T. / Wisely, G.B. / Westin, S. / Cobb, J.E. / Lambert, M.H. / Kurokawa, R. / Rosenfeld, M.G. / Willson, T.M. / Glass, C.K. / Milburn, M.V.
History
DepositionAug 14, 1998Processing site: BNL
Revision 1.0Jul 19, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
B: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
C: NUCLEAR RECEPTOR COACTIVATOR SRC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1055
Polymers71,3903
Non-polymers7152
Water9,746541
1
A: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3542
Polymers30,9971
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-6 kcal/mol
Surface area13850 Å2
MethodPISA
2
B: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
C: NUCLEAR RECEPTOR COACTIVATOR SRC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7513
Polymers40,3932
Non-polymers3571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-14 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.210, 69.061, 177.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6963, -0.4441, 0.5639), (-0.5229, -0.2244, -0.8223), (0.4917, -0.8674, -0.076)
Vector: 68.3446, 24.7629, -15.4209)

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Components

#1: Protein PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA / E DOMAIN


Mass: 30997.021 Da / Num. of mol.: 2 / Fragment: LBD (LIGAND BINDING DOMAIN), RESIDUES 207-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUSCell nucleus / Gene: HUMAN PPAR GAMMA CDNA / Plasmid: PRSET A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): HPPARGAMMA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P37231
#2: Protein NUCLEAR RECEPTOR COACTIVATOR SRC-1


Mass: 9396.225 Da / Num. of mol.: 1 / Fragment: FRAGMENT CONTAINING HD1 & HD2 RESIDUES 628-703
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH ROSIGLITAZONE (BRL-49653) REGISTRY # 122320-73-4
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUSCell nucleus / Gene: SRC-1 CDNA / Plasmid: PRSET A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O43792, UniProt: Q15788*PLUS
#3: Chemical ChemComp-BRL / 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) / BRL49653 / ROSIGLITAZONE / Rosiglitazone


Mass: 357.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N3O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
225 mMTris-HCl1drop
35 mMdithiothreitol1drop
4500 mMammonium acetate1drop
517 %PEG40001reservoir
6200 mMammonium acetate1reservoir
720 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 26501 / % possible obs: 89.7 % / Observed criterion σ(I): -3 / Redundancy: 3.42 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.185 / % possible all: 58.3
Reflection shell
*PLUS
% possible obs: 58.3 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PRG

1prg


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 266280597.97 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 653 2.5 %RANDOM
Rwork0.207 ---
obs0.207 26436 89.9 %-
Solvent computationSolvent model: SHRINK MASK | SHELL MODEL / Bsol: 120 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.38 Å20 Å20 Å2
2---4.56 Å20 Å2
3---12.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 86 541 5040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_mcangle_it3.482
X-RAY DIFFRACTIONc_scbond_it6.162
X-RAY DIFFRACTIONc_scangle_it7.512.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 65 2.3 %
Rwork0.226 2745 -
obs--58.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BSXPI_FIXDBLE.XPL
X-RAY DIFFRACTION4LOCALPARM.XPL

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