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- PDB-7rle: Crystal structure of PPAR gamma in complex with CREB-binding prot... -

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Basic information

Entry
Database: PDB / ID: 7rle
TitleCrystal structure of PPAR gamma in complex with CREB-binding protein and agonist GW1929
Components
  • CREB-binding protein
  • Peroxisome proliferator-activated receptor gamma
KeywordsDNA BINDING PROTEIN / Nuclear Receptor / Transcription Factor
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / 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 / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / negative regulation of vascular endothelial cell proliferation / RUNX3 regulates NOTCH signaling / negative regulation of cellular response to transforming growth factor beta stimulus / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of cardiac muscle hypertrophy in response to stress / Regulation of NFE2L2 gene expression / arachidonate binding / positive regulation of low-density lipoprotein receptor activity / negative regulation of transcription by RNA polymerase I / positive regulation of adiponectin secretion / NOTCH3 Intracellular Domain Regulates Transcription / lipoprotein transport / negative regulation of sequestering of triglyceride / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / DNA binding domain binding / macrophage derived foam cell differentiation / embryonic digit morphogenesis / STAT family protein binding / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of fatty acid metabolic process / response to lipid / homeostatic process / protein acetylation / negative regulation of SMAD protein signal transduction / LBD domain binding / Notch-HLH transcription pathway / negative regulation of type II interferon-mediated signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cholesterol storage / Formation of paraxial mesoderm / E-box binding / alpha-actinin binding / acetyltransferase activity / lipid homeostasis / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / Attenuation phase / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / retinoic acid receptor signaling pathway / cell fate commitment / cellular response to nutrient levels / BMP signaling pathway / long-chain fatty acid transport / canonical NF-kappaB signal transduction / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / regulation of cellular response to heat / histone acetyltransferase activity / histone acetyltransferase / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Peroxisome proliferator-activated receptor / : / Nuclear receptor coactivator, interlocking / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-EDK / Peroxisome proliferator-activated receptor gamma / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNemetchek, M.D. / Sprang, S.R. / Hughes, T.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R00DK103116 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: A structural mechanism of nuclear receptor biased agonism.
Authors: Nemetchek, M.D. / Chrisman, I.M. / Rayl, M.L. / Voss, A.H. / Hughes, T.S.
History
DepositionJul 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: CREB-binding protein
C: Peroxisome proliferator-activated receptor gamma
D: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8566
Polymers67,8654
Non-polymers9912
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-15 kcal/mol
Surface area25660 Å2
Unit cell
Length a, b, c (Å)59.890, 99.422, 109.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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.: 2
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 CREB-binding protein / Histone lysine acetyltransferase CREBBP / Protein-lysine acetyltransferase CREBBP


Mass: 2425.699 Da / Num. of mol.: 2 / Fragment: Residues 57-80 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q92793, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#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.: 2 / Source method: obtained synthetically / Formula: C30H29N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.9 % / Description: 100um x 50um pentagonal prisms
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→49.71 Å / Num. obs: 22792 / % possible obs: 98.19 % / Redundancy: 11.6 % / Biso Wilson estimate: 57.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1343 / Rpim(I) all: 0.04009 / Rrim(I) all: 0.1404 / Net I/σ(I): 13.49
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.5342 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2104 / CC1/2: 0.737 / CC star: 0.921 / Rpim(I) all: 0.2083 / Rrim(I) all: 0.5765 / % possible all: 93.02

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D94

6d94


Resolution: 2.5→49.71 Å / SU ML: 0.3388 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 29.0831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2749 1594 6.99 %
Rwork0.2323 21198 -
obs0.2353 22792 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.48 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4451 0 74 23 4548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794602
X-RAY DIFFRACTIONf_angle_d1.20816190
X-RAY DIFFRACTIONf_chiral_restr0.0673708
X-RAY DIFFRACTIONf_plane_restr0.0098783
X-RAY DIFFRACTIONf_dihedral_angle_d17.96471739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.31231330.2811771X-RAY DIFFRACTION92.74
2.58-2.670.33721390.28061852X-RAY DIFFRACTION96.56
2.67-2.780.35531430.27631893X-RAY DIFFRACTION97.98
2.78-2.910.36511450.26971935X-RAY DIFFRACTION99.62
2.91-3.060.31731470.28171943X-RAY DIFFRACTION99.76
3.06-3.250.31731430.27631911X-RAY DIFFRACTION98.89
3.25-3.50.31521440.26371907X-RAY DIFFRACTION97.62
3.5-3.850.28121460.23411954X-RAY DIFFRACTION99.67
3.85-4.410.27751480.20271958X-RAY DIFFRACTION99.06
4.41-5.560.21861510.21332004X-RAY DIFFRACTION99.68
5.56-49.710.24241550.2082070X-RAY DIFFRACTION98.63
Refinement TLS params.Method: refined / Origin x: -25.682983496 Å / Origin y: 15.0090468547 Å / Origin z: -29.2334192563 Å
111213212223313233
T0.344242158084 Å2-0.0310357471526 Å20.0962608541502 Å2-0.322364594156 Å2-0.0512055383416 Å2--0.478917886588 Å2
L2.45497950736 °2-0.636290436233 °20.710081463161 °2-1.80378864937 °2-1.09384974053 °2--2.86270757583 °2
S-0.104438702385 Å °0.0075113841636 Å °0.272312597122 Å °-0.0819808407579 Å °0.00263898070697 Å °-0.31551325354 Å °-0.0805439894097 Å °0.36213758843 Å °0.097690781328 Å °
Refinement TLS groupSelection details: all

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