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- PDB-1i7g: CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN FROM HUMAN PPAR-AL... -

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Entry
Database: PDB / ID: 1i7g
TitleCRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN FROM HUMAN PPAR-ALPHA IN COMPLEX WITH THE AGONIST AZ 242
ComponentsPEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA
KeywordsTRANSCRIPTION / Anti parallel Helix Sandwich
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / positive regulation of fatty acid beta-oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite / negative regulation of hepatocyte apoptotic process ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / positive regulation of fatty acid beta-oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite / negative regulation of hepatocyte apoptotic process / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / negative regulation of leukocyte cell-cell adhesion / negative regulation of glycolytic process / ubiquitin conjugating enzyme binding / mitogen-activated protein kinase kinase kinase binding / positive regulation of fatty acid metabolic process / DNA-binding transcription activator activity / NFAT protein binding / negative regulation of cholesterol storage / positive regulation of ATP biosynthetic process / nuclear steroid receptor activity / negative regulation of macrophage derived foam cell differentiation / epidermis development / phosphatase binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / intracellular receptor signaling pathway / negative regulation of blood pressure / nitric oxide metabolic process / hormone-mediated signaling pathway / negative regulation of reactive oxygen species biosynthetic process / : / Regulation of lipid metabolism by PPARalpha / response to nutrient / peroxisome proliferator activated receptor signaling pathway / MDM2/MDM4 family protein binding / positive regulation of gluconeogenesis / negative regulation of cytokine production involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / cellular response to starvation / gluconeogenesis / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / fatty acid metabolic process / wound healing / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / response to insulin / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / nuclear receptor activity / : / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / lipid binding / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / 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. ...Peroxisome proliferator-activated receptor alpha / 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-AZ2 / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPetersen, J.F.W. / Cronet, P. / Folmer, R. / Blomberg, N. / Sjoblom, K. / Karlsson, U. / Lindstedt, E.-L. / Bamberg, K.
CitationJournal: Structure / Year: 2001
Title: Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family.
Authors: Cronet, P. / Petersen, J.F. / Folmer, R. / Blomberg, N. / Sjoblom, K. / Karlsson, U. / Lindstedt, E.L. / Bamberg, K.
History
DepositionMar 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6314
Polymers32,3371
Non-polymers1,2943
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.968, 76.968, 100.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA / PPAR-ALPHA


Mass: 32337.348 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AZ2 / (2S)-2-ETHOXY-3-[4-(2-{4-[(METHYLSULFONYL)OXY]PHENYL}ETHOXY)PHENYL]PROPANOIC ACID / AZ 242


Mass: 408.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24O7S / Comment: agonist*YM
#4: Chemical ChemComp-CPQ / N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE / DEOXY-BIGCHAP


Mass: 862.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H75N3O15 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Sodium Formate, Hepes, DEOXY-BIGCHAP, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17 mg/mlprotein1drop
220 mMTris1drop
3150 mM1dropNaCl
410 %glycerol1drop
51 mMTCEP1droppH8.
60.5 mMligand AZ 2421drop
73.2 Msodium formate1reservoir
8100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9465 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9465 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. obs: 17036 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 5
Reflection shellResolution: 2.24→2.39 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
EPMRphasing
CNX2000refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 2PRG A molecule

2prg


Resolution: 2.2→23.64 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2276975.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.271 868 4.9 %RANDOM
Rwork0.237 ---
obs-17852 99.3 %-
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.35 Å24.53 Å20 Å2
2--8.35 Å20 Å2
3----16.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 54 70 2188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
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_it0.81.5
X-RAY DIFFRACTIONc_mcangle_it1.412
X-RAY DIFFRACTIONc_scbond_it1.062
X-RAY DIFFRACTIONc_scangle_it1.662.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 145 5 %
Rwork0.289 2768 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PPARA.PARPPARA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAMION.TOP
X-RAY DIFFRACTION5ION.PARAM
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it0.81.5
X-RAY DIFFRACTIONc_scbond_it1.062
X-RAY DIFFRACTIONc_mcangle_it1.412
X-RAY DIFFRACTIONc_scangle_it1.662.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.352 / % reflection Rfree: 5 % / Rfactor Rwork: 0.289

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