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- PDB-9ck0: Cocrystal of PPARg LBD and NFKBIB / IKBB peptide with agonist GW1929 -

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Basic information

Entry
Database: PDB / ID: 9ck0
TitleCocrystal of PPARg LBD and NFKBIB / IKBB peptide with agonist GW1929
Components
  • NF-kappa-B inhibitor beta
  • Peroxisome proliferator-activated receptor gamma
KeywordsDNA BINDING PROTEIN / Nuclear Receptor / PPARg / PPAR gamma / Alpha Helix / NFKB / NFKB inhibitor / inflammation / type II diabetes
Function / homology
Function and homology information


RIP-mediated NFkB activation via ZBP1 / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / regulation of canonical NF-kappaB signal transduction / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus ...RIP-mediated NFkB activation via ZBP1 / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / regulation of canonical NF-kappaB signal transduction / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / TRAF6 mediated NF-kB activation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / negative regulation of MAPK cascade / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / Activation of NF-kappaB in B cells / mRNA transcription by RNA polymerase II / PPARA activates gene expression / TAK1-dependent IKK and NF-kappa-B activation / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / regulation of blood pressure / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Ankyrin repeats (many copies) / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...Ankyrin repeats (many copies) / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing 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
Similarity search - Domain/homology
Chem-EDK / Peroxisome proliferator-activated receptor gamma / NF-kappa-B inhibitor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNemetchek, M.D. / McClelland, L.J. / Hughes, T.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK129646 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 United States
CitationJournal: To Be Published
Title: Cocrystal of PPARg LBD with NFKBIB / IKBB peptide containing N-anchor motif LxxLL and agonist GW1929
Authors: Nemetchek, M.D. / Hughes, T.S.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: 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: NF-kappa-B inhibitor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4283
Polymers33,9332
Non-polymers4961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.530, 89.500, 121.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 31506.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide NF-kappa-B inhibitor beta / NF-kappa-BIB / I-kappa-B-beta / IkB-B / IkB-beta / IkappaBbeta / Thyroid receptor-interacting ...NF-kappa-BIB / I-kappa-B-beta / IkB-B / IkB-beta / IkappaBbeta / Thyroid receptor-interacting protein 9 / TR-interacting protein 9 / TRIP-9


Mass: 2425.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15653
#3: Chemical ChemComp-EDK / (2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid


Mass: 495.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H29N3O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.71 % / Description: Trapezoidal plates
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M LIthium sulfate, 0.1 M Tris pH 8.5, 16% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→30.27 Å / Num. obs: 9494 / % possible obs: 98.3 % / Redundancy: 7.8 % / Biso Wilson estimate: 55.13 Å2 / Rrim(I) all: 0.14 / Net I/σ(I): 12.4
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 879 / Rrim(I) all: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30.27 Å / SU ML: 0.3647 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 31.7062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2958 960 10.12 %
Rwork0.2499 8530 -
obs0.2546 9490 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.74 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 37 0 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712307
X-RAY DIFFRACTIONf_angle_d1.27073115
X-RAY DIFFRACTIONf_chiral_restr0.076361
X-RAY DIFFRACTIONf_plane_restr0.0089395
X-RAY DIFFRACTIONf_dihedral_angle_d17.1905862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.36331400.341120X-RAY DIFFRACTION93.75
2.74-2.910.31751350.31551210X-RAY DIFFRACTION98.03
2.91-3.130.39821300.32081207X-RAY DIFFRACTION99.33
3.13-3.450.34451360.29021228X-RAY DIFFRACTION99.85
3.45-3.950.30131370.2661225X-RAY DIFFRACTION99.13
3.95-4.970.26371450.21421238X-RAY DIFFRACTION99.71
4.97-30.270.26421370.2081302X-RAY DIFFRACTION98.63
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.518618715410.3693419334580.3313364350063.908061538941.246233694813.38712369785-0.0866430055118-0.3576006617060.07586763953890.4602785365230.289589141542-0.405418713078-0.1887595201710.475618959137-0.1948575871990.4010942712590.0500505541623-0.05970204879510.496398768407-0.03008350124570.313366823955-22.5526956672-9.7568287015816.2388358733
25.67879293786-2.946144033390.31832244199.80097561625-1.453012414555.56484235687-0.494898925863-0.480636058015-0.4116748057621.122137424510.410063700597-0.3963886873660.3528003217880.738845712978-0.03364759851940.4334365937820.0308276005383-0.05084511358280.530023836119-0.02114765679220.386513351309-19.8892865425-20.007778312321.1027857018
32.00074020599-5.88200043065-0.6298844355976.497279208661.756370766522.00263834134-0.07986972903061.013299315150.3140520303190.839547099037-0.682821963422-1.01178374803-1.115757797650.847001904570.7557895122090.685262773045-0.0201007452025-0.07338043189260.7614336728590.1976454320420.913552004713-3.22395854801-12.623541037813.4902026457
48.807313391856.943027012793.866112417235.456640597252.614607462735.28154814066-0.5060612830960.2870665464690.563329918799-0.7477471013260.3756752950040.254247225991-0.7749487957960.01251658830670.1091898780440.4226019696520.06281062322190.02910818395910.3964334940710.01565536213990.330270889087-28.0270588611-7.846616425054.04441117233
58.25574970545-1.63542407902-5.228065595130.5680461608092.115498816128.08064241346-0.176033394276-0.931667103069-0.505573297166-0.2923977517120.1394904210110.4881007808311.11806728609-0.7899776070890.05006104682590.440557646462-0.109029950333-0.06391505388950.663358203817-0.0003107801387760.462029987879-19.6714967811-28.9826574324-1.01975444318
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 277 through 430 )AA277 - 43070 - 223
22chain 'A' and (resid 431 through 477 )AA431 - 477224 - 270
33chain 'B' and (resid 287 through 297 )BC287 - 2971 - 11
44chain 'A' and (resid 208 through 261 )AA208 - 2611 - 54
55chain 'A' and (resid 262 through 276 )AA262 - 27655 - 69

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