[English] 日本語
Yorodumi
- PDB-7cxk: The ligand-free structure of human PPARgamma LBD R288H mutant in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cxk
TitleThe ligand-free structure of human PPARgamma LBD R288H mutant in the presence of the SRC-1 coactivator peptide
Components
  • 16-mer peptide from Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor / ligand binding domain / mutant
Function / homology
Function and homology information


labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / 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 ...labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / 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 / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / positive regulation of fatty acid metabolic process / STAT family protein binding / male mating behavior / response to lipid / negative regulation of type II interferon-mediated signaling pathway / hypothalamus development / LBD domain binding / negative regulation of cholesterol storage / negative regulation of SMAD protein signal transduction / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / cellular response to Thyroglobulin triiodothyronine / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / Synthesis of bile acids and bile salts / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / progesterone receptor signaling pathway / negative regulation of lipid storage / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cell fate commitment / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / BMP signaling pathway / long-chain fatty acid transport / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / retinoic acid receptor signaling pathway / cell maturation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of MAPK cascade / intracellular receptor signaling pathway / estrogen receptor signaling pathway / hormone-mediated signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / response to nutrient / epithelial cell differentiation / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / negative regulation of miRNA transcription / cerebellum development / negative regulation of angiogenesis / placenta development / nuclear estrogen receptor binding / nuclear receptor binding / Regulation of PTEN gene transcription / positive regulation of apoptotic signaling pathway / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / Heme signaling / negative regulation of transforming growth factor beta receptor signaling pathway
Similarity search - Function
Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / 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 ...Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS 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
MALONATE ION / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJang, D.M. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2011-0030001 Korea, Republic Of
CitationJournal: To Be Published
Title: The ligand-free structure of human PPARgamma LBD
Authors: Jang, D.M. / Han, B.W.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: 16-mer peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2693
Polymers34,1662
Non-polymers1021
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.396, 51.997, 54.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

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


Mass: 32261.303 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 16-mer peptide from Nuclear receptor coactivator 1


Mass: 1905.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2 M sodium malonate (pH 7.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 19382 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Net I/σ(I): 31.63
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 4.31 / Num. unique obs: 963 / CC1/2: 0.92 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GTP

5gtp


Resolution: 2.2→36.041 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.737 / SU ML: 0.165 / Cross valid method: FREE R-VALUE / ESU R: 0.267 / ESU R Free: 0.209
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2636 945 4.901 %
Rwork0.2369 18338 -
all0.238 --
obs-19283 99.53 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.259 Å20 Å20 Å2
2--0.132 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 7 77 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132263
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172206
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6363044
X-RAY DIFFRACTIONr_angle_other_deg1.2211.5795135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7823.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82915444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.997159
X-RAY DIFFRACTIONr_chiral_restr0.0670.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined0.2120.2538
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21935
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21104
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.211
X-RAY DIFFRACTIONr_nbd_other0.2370.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.23
X-RAY DIFFRACTIONr_mcbond_it3.0183.8481097
X-RAY DIFFRACTIONr_mcbond_other3.0133.8441096
X-RAY DIFFRACTIONr_mcangle_it4.9675.7391366
X-RAY DIFFRACTIONr_mcangle_other4.9675.7441367
X-RAY DIFFRACTIONr_scbond_it3.1354.3011166
X-RAY DIFFRACTIONr_scbond_other3.1374.2941164
X-RAY DIFFRACTIONr_scangle_it5.276.251677
X-RAY DIFFRACTIONr_scangle_other5.276.251677
X-RAY DIFFRACTIONr_lrange_it8.10145.152551
X-RAY DIFFRACTIONr_lrange_other8.145.1822552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.362470.2951365X-RAY DIFFRACTION98.4658
2.257-2.3190.289630.2961254X-RAY DIFFRACTION98.9482
2.319-2.3860.321670.2731262X-RAY DIFFRACTION99.8497
2.386-2.4590.385580.2971234X-RAY DIFFRACTION100
2.459-2.540.299550.2641197X-RAY DIFFRACTION100
2.54-2.6280.32710.2881140X-RAY DIFFRACTION100
2.628-2.7270.319630.2821136X-RAY DIFFRACTION100
2.727-2.8380.349700.2631050X-RAY DIFFRACTION99.9108
2.838-2.9640.366500.271043X-RAY DIFFRACTION100
2.964-3.1080.332450.2581001X-RAY DIFFRACTION100
3.108-3.2760.231500.24957X-RAY DIFFRACTION100
3.276-3.4730.252400.234901X-RAY DIFFRACTION100
3.473-3.7120.216480.222849X-RAY DIFFRACTION100
3.712-4.0080.209530.206777X-RAY DIFFRACTION99.7596
4.008-4.3870.213360.185744X-RAY DIFFRACTION100
4.387-4.90.181390.182663X-RAY DIFFRACTION100
4.9-5.6490.198250.217612X-RAY DIFFRACTION100
5.649-6.8970.282330.228509X-RAY DIFFRACTION100
6.897-9.6630.164160.164405X-RAY DIFFRACTION96.7816
9.663-36.0410.293160.263231X-RAY DIFFRACTION87.9004

+
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