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- PDB-5dv6: Human PPARgamma ligand binding dmain complexed with SB1404 in a c... -

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Basic information

Entry
Database: PDB / ID: 5dv6
TitleHuman PPARgamma ligand binding dmain complexed with SB1404 in a covalent bonded form
Components
  • Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION/TRANSFERASE / PPARgamma / antagonist / TRANSCRIPTION-TRANSFERASE complex
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Complex I biogenesis / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Respiratory electron transport / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / response to retinoic acid / mitochondrial ATP synthesis coupled electron transport / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / mitochondrial respiratory chain complex I assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / NADH dehydrogenase (ubiquinone) activity / hippocampus development / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitochondrial membrane / aerobic respiration / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / cerebral cortex development / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / protein dimerization activity / mitochondrial inner membrane / positive regulation of apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor coactivator 1 / 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 ...Nuclear receptor coactivator 1 / 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 / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / 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 / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
N-methylidene-3-nitrobenzamide / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsJang, J.Y.
CitationJournal: To Be Published
Title: Human PPARgamma ligand binding dmain complexed with SB1404 in a covalent bonded form
Authors: Jang, J.Y.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7773
Polymers34,5992
Non-polymers1781
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.383, 130.851, 53.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 32693.824 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 223-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P37231
#2: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1905.186 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 685-700 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-B4H / N-methylidene-3-nitrobenzamide


Mass: 178.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9332 / % possible obs: 98.9 % / Redundancy: 5.5 % / Net I/σ(I): 35.05
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.19 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.17 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 1.981 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24409 466 4.9 %RANDOM
Rwork0.20801 ---
obs0.20967 9137 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å2-0 Å2
2---5.83 Å20 Å2
3---5.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 13 32 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192241
X-RAY DIFFRACTIONr_bond_other_d0.0060.022245
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9943017
X-RAY DIFFRACTIONr_angle_other_deg0.98635179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60925.15299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84415438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.11159
X-RAY DIFFRACTIONr_chiral_restr0.080.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022448
X-RAY DIFFRACTIONr_gen_planes_other0.010.02481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4537.8841083
X-RAY DIFFRACTIONr_mcbond_other5.4537.8811082
X-RAY DIFFRACTIONr_mcangle_it8.14211.7981349
X-RAY DIFFRACTIONr_mcangle_other8.13911.81350
X-RAY DIFFRACTIONr_scbond_it5.8978.6271158
X-RAY DIFFRACTIONr_scbond_other5.8958.6271159
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.30412.6421668
X-RAY DIFFRACTIONr_long_range_B_refined12.9762.9862601
X-RAY DIFFRACTIONr_long_range_B_other12.96162.9892601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 31 -
Rwork0.223 644 -
obs--98.97 %

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