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- PDB-1k7l: The 2.5 Angstrom resolution crystal structure of the human PPARal... -

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Basic information

Entry
Database: PDB / ID: 1k7l
TitleThe 2.5 Angstrom resolution crystal structure of the human PPARalpha ligand binding domain bound with GW409544 and a co-activator peptide.
Components
  • Peroxisome proliferator activated receptor alpha
  • steroid receptor coactivator
KeywordsTRANSCRIPTION / The 2.5 Angstrom resolution crystal structure of the human PPARalpha ligand binding domain bound with GW409544 and a coactivator peptide
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / negative regulation of hepatocyte apoptotic process / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / positive regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / DNA-binding transcription activator activity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / cellular response to Thyroglobulin triiodothyronine / negative regulation of macrophage derived foam cell differentiation / Synthesis of bile acids and bile salts / epidermis development / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / phosphatase binding / response to retinoic acid / positive regulation of lipid biosynthetic process / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / estrogen receptor signaling pathway / nitric oxide metabolic process / negative regulation of blood pressure / positive regulation of adipose tissue development / hormone-mediated signaling pathway / : / MDM2/MDM4 family protein binding / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of cytokine production involved in inflammatory response / response to nutrient / positive regulation of gluconeogenesis / positive regulation of neuron differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / hippocampus development / response to progesterone / cellular response to starvation / nuclear receptor binding / gluconeogenesis / fatty acid metabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / response to insulin / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / 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 ...Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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-544 / YTTRIUM (III) ION / Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsXu, H.E. / Lambert, M.H. / Montana, V.G. / Moore, L.B. / Collins, J.L. / Oplinger, J.A. / Kliewer, S.A. / Gampe Jr., R.T. / McKee, D.D. / Moore, J.T. / Willson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors.
Authors: Xu, H.E. / Lambert, M.H. / Montana, V.G. / Plunket, K.D. / Moore, L.B. / Collins, J.L. / Oplinger, J.A. / Kliewer, S.A. / Gampe Jr., R.T. / McKee, D.D. / Moore, J.T. / Willson, T.M.
History
DepositionOct 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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 / software / 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 / _software.classification / _software.name / _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

Downloads & links

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Assembly

Deposited unit
A: Peroxisome proliferator activated receptor alpha
B: steroid receptor coactivator
C: Peroxisome proliferator activated receptor alpha
D: steroid receptor coactivator
E: Peroxisome proliferator activated receptor alpha
F: steroid receptor coactivator
G: Peroxisome proliferator activated receptor alpha
H: steroid receptor coactivator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,87114
Polymers140,6518
Non-polymers2,2206
Water4,360242
1
A: Peroxisome proliferator activated receptor alpha
B: steroid receptor coactivator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6733
Polymers35,1632
Non-polymers5111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-26 kcal/mol
Surface area13320 Å2
MethodPISA
2
C: Peroxisome proliferator activated receptor alpha
D: steroid receptor coactivator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7624
Polymers35,1632
Non-polymers5992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-26 kcal/mol
Surface area13150 Å2
MethodPISA
3
E: Peroxisome proliferator activated receptor alpha
F: steroid receptor coactivator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7624
Polymers35,1632
Non-polymers5992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-24 kcal/mol
Surface area13120 Å2
MethodPISA
4
G: Peroxisome proliferator activated receptor alpha
H: steroid receptor coactivator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6733
Polymers35,1632
Non-polymers5111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-23 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.561, 121.597, 121.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peroxisome proliferator activated receptor alpha / PPARalpha


Mass: 32731.014 Da / Num. of mol.: 4 / Fragment: ligand binding domain - residues 192 - 468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: T7 promoter control plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) E.Coli / References: UniProt: Q07869
#2: Protein/peptide
steroid receptor coactivator


Mass: 2431.750 Da / Num. of mol.: 4 / Fragment: src-1 peptide / Source method: obtained synthetically
Details: Chemically synthesized 21mer portion of the the human src-1 coactivator peptide.
References: UniProt: O43792, UniProt: Q15788*PLUS
#3: Chemical
ChemComp-544 / 2-(1-METHYL-3-OXO-3-PHENYL-PROPYLAMINO)-3-{4-[2-(5-METHYL-2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID / GW409544


Mass: 510.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H30N2O5
#4: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, NaNO3, hexanediol, YCl3, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMbis-Tris-propane1reservoirpH7.5
24-6 %PEG33501reservoir
3150 mM1reservoirNaNO3
416 %2,5-hexanediol1reservoir
51-3 mM1reservoirYCl3
6220 mMammonium acetate1drop
720 mMHEPES1droppH7.5
81 mMEDTA1drop
91 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 49991 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 52.8 Å2 / Rsym value: 0.054
Reflection
*PLUS
Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Mean I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
AMoREphasing
CNX2000.1refinement
MAR345data collection
HKL-2000data scaling
RefinementResolution: 2.5→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 318526.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 4018 8.2 %RANDOM
Rwork0.247 ---
obs-48912 98.3 %-
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.29 Å20 Å20 Å2
2---4.61 Å20 Å2
3----2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8912 0 154 242 9308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 663 8.5 %
Rwork0.308 7106 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3bsxpi3.xpl
X-RAY DIFFRACTION4y.para
X-RAY DIFFRACTION5544.xpl
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.247 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / Rfactor Rwork: 0.308

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