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- PDB-9cwn: NRIP1_133 / RIP140 SxxLxxLL motif coregulator peptide with agonis... -

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Basic information

Entry
Database: PDB / ID: 9cwn
TitleNRIP1_133 / RIP140 SxxLxxLL motif coregulator peptide with agonist GW1929 and PPARg LBD
Components
  • Nuclear receptor-interacting protein 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsDNA BINDING PROTEIN / Nuclear Receptor / Transcription Factor / Coregulator / cofactor / NRIP1 / RIP140 / PPARg / PPARgamma
Function / homology
Function and homology information


ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / 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 ...ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / 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 / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonate binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / STAT family protein binding / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / histone deacetylase complex / 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 / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / retinoic acid receptor signaling pathway / cell fate commitment / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / cellular response to estradiol stimulus / transcription coregulator binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / fibrillar center / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / histone deacetylase binding / negative regulation of inflammatory response / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / circadian rhythm / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / transcription corepressor activity / nuclear receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / Circadian Clock / rhythmic process / glucose homeostasis / cellular response to hypoxia
Similarity search - Function
Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Peroxisome proliferator-activated receptor gamma ...Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / 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
Similarity search - Domain/homology
Chem-EDK / Peroxisome proliferator-activated receptor gamma / Nuclear receptor-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNemetchek, M.D. / Voss, A.H. / 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: NRIP1_133 / RIP140 SxxLxxLL motif coregulator peptide with agonist GW1929 and PPARg LBD
Authors: Nemetchek, M.D. / Voss, A.H. / Hughes, T.S.
History
DepositionJul 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,5303
Polymers34,0342
Non-polymers4961
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer, Agonist-induced binding as seen by TR-FRET
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.236, 118.815, 151.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-733-

HOH

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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 Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 2527.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P48552
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.05 Å3/Da / Density % sol: 69.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.6 M AmSO4, 100mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→32.57 Å / Num. obs: 13880 / % possible obs: 94.65 % / Redundancy: 2 % / Biso Wilson estimate: 48.94 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.05921 / Rpim(I) all: 0.05921 / Rrim(I) all: 0.08373 / Net I/σ(I): 10.63
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.4223 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 948 / CC1/2: 0.637 / CC star: 0.882 / Rpim(I) all: 0.4223 / Rrim(I) all: 0.5972

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092phasing
XDSJun 30, 2023 (BUILT 20230630)data reduction
STARANISO2.3.79 (20211010)data scaling
autoPROCautoPROC 1.0.5 (20211020)data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→32.57 Å / SU ML: 0.2432 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242 747 5.38 %
Rwork0.1977 13129 -
obs0.2001 13876 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 37 45 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452295
X-RAY DIFFRACTIONf_angle_d0.93933095
X-RAY DIFFRACTIONf_chiral_restr0.0501360
X-RAY DIFFRACTIONf_plane_restr0.0036391
X-RAY DIFFRACTIONf_dihedral_angle_d16.2311863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.33791200.2652018X-RAY DIFFRACTION74.39
2.91-3.20.32951630.26162703X-RAY DIFFRACTION99.41
3.2-3.660.25631520.21552741X-RAY DIFFRACTION99.93
3.66-4.610.22111410.16962788X-RAY DIFFRACTION99.76
4.61-32.570.20031710.17552879X-RAY DIFFRACTION99.67
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)
17.49749845693-1.226815161011.954976068289.30247198499-2.675561451767.22466249934-0.517576304098-0.4703117660090.8222846522130.8916417541620.152412868249-0.516265926207-1.58639371532-0.01583907549690.3711968436120.5651947840930.0039677431212-0.01645304753080.264257539355-0.06757954494510.2715060002372.2458052206521.588036882161.6885334814
26.46966199995-0.128396836751-3.48250589457.29299910633-2.296410812422.00161325938-0.110672000836-0.1451941502111.015562068690.200437939604-0.250520716574-0.531460381361-1.921981805860.4176819417280.3643195280870.6639148690610.139803841531-0.1886273703960.4841359732430.102224337730.802303773265-10.691194122232.518944303941.2955362868
34.87224595150.3993514473561.290541344030.1309802467480.02703555123780.403873533034-0.280833066905-0.5551058768210.957246243675-0.8609499458230.7205939678030.535298249057-1.36345314172-1.24124630285-0.4400984152690.9924185685540.0391384744128-0.1340717651591.11055920406-0.001105795050551.001012674843.2236932162330.573713971130.3720363443
44.26720459523-0.6178122027460.2678406902413.17651478654-0.2766678938415.35658453636-0.04761015742260.2202605260490.129003439168-0.040096127712-0.102650355689-0.083863033895-0.2293277462110.1372495152320.1563556395720.262807009554-0.0589120101494-0.02155940303680.1233390154680.01003352075310.2654953862792.1622644328213.995533839350.7530998149
55.54403100777-0.200575618885-0.8157223827344.508758197611.297064720456.55443535341-0.2700768357141.05096073629-0.138707672718-1.1614415389-0.022303666227-0.319581491290.8236461580080.008430412506610.3101684577150.4179608711560.0116250243654-0.007288071239650.3604335900150.0006857002707190.3293872939673.736242406178.9597789658340.063379373
62.00132713353-8.3779786732-1.961736345948.147805442297.83667875692.0011088441-0.177186712728-0.2476633803220.4477043563660.001472147962080.753377799126-1.61072811025-0.6749189161882.52957009852-0.5655634833010.471514169864-0.154377104667-0.04577284543520.791245526890.2084087758730.76963656842120.523065573518.834790549545.8784156045
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 237 through 265 )AA237 - 2652 - 30
22chain 'A' and (resid 266 through 289 )AA266 - 28931 - 54
33chain 'A' and (resid 290 through 304 )AA290 - 30455 - 66
44chain 'A' and (resid 305 through 458 )AA305 - 45867 - 220
55chain 'A' and (resid 459 through 505 )AA459 - 505221 - 267
66chain 'B' and (resid 130 through 139 )BC130 - 1391 - 10

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