[English] 日本語
Yorodumi
- PDB-9cwn: NRIP1_133 / RIP140 SxxLxxLL motif coregulator peptide with agonis... -

+
Open data


ID or keywords:

Loading...

-
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 / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation ...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 / : / 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 / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / DNA binding domain binding / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / positive regulation of fatty acid metabolic process / STAT family protein binding / 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 / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / histone deacetylase complex / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / cell fate commitment / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / 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 / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / response to nutrient / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / negative regulation of angiogenesis / placenta development / Regulation of PTEN gene transcription / positive regulation of apoptotic signaling pathway / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / fatty acid metabolic process / Heme signaling / PPARA activates gene expression / regulation of circadian rhythm / circadian rhythm / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / lipid metabolic process / regulation of blood pressure / positive regulation of miRNA transcription / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / histone deacetylase binding / fibrillar center / cellular response to insulin stimulus / nuclear receptor activity / : / rhythmic process / transcription corepressor activity / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more