[English] 日本語
Yorodumi
- PDB-4xum: PPARgamma ligand binding domain in complex with indomethacin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xum
TitlePPARgamma ligand binding domain in complex with indomethacin
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSLATION / PPARgamma / Nuclear receptor / transcription factor / NSAIDs / indomethacin
Function / homology
Function and homology information


prostaglandin receptor 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 / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity ...prostaglandin receptor 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 / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / 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 / 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 / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / epithelial cell differentiation / negative regulation of signaling receptor activity / 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 / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / transcription coregulator binding / fatty acid metabolic process / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / regulation of blood pressure / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
INDOMETHACIN / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPuhl, A.C. / Webb, P. / Polikarpov, I.
CitationJournal: Nucl Recept Signal / Year: 2015
Title: Mechanisms of peroxisome proliferator activated receptor gamma regulation by non-steroidal anti-inflammatory drugs.
Authors: Puhl, A.C. / Milton, F.A. / Cvoro, A. / Sieglaff, D.H. / Campos, J.C. / Bernardes, A. / Filgueira, C.S. / Lindemann, J.L. / Deng, T. / Neves, F.A. / Polikarpov, I. / Webb, P.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5435
Polymers63,4702
Non-polymers1,0733
Water1,18966
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4503
Polymers31,7351
Non-polymers7162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0932
Polymers31,7351
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.040, 62.140, 118.540
Angle α, β, γ (deg.)90.000, 102.130, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 207 - 477 / Label seq-ID: 8 - 278

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

-
Components

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


Mass: 31734.863 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: Chemical ChemComp-IMN / INDOMETHACIN


Mass: 357.788 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.95 M sodium citrate and 0.1 M HEPES pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.4→115.893 Å / Num. all: 26080 / Num. obs: 26080 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 51.11 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.079 / Rsym value: 0.069 / Net I/av σ(I): 6.683 / Net I/σ(I): 12.1 / Num. measured all: 116570
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.534.40.5021.51684837990.2730.5022.8100
2.53-2.684.40.3312.31598935970.1790.3314100
2.68-2.874.50.2113.51486333300.1150.2116100
2.87-3.14.50.1435.11421231700.0770.1438.4100
3.1-3.394.50.08281295728790.0450.08213.3100
3.39-3.794.50.0639.11184126180.0340.06318.2100
3.79-4.384.50.06191057223380.0330.06122.4100
4.38-5.374.50.05810.1892919790.0310.05823.8100
5.37-7.594.50.04711.9689615350.0250.04724.1100
7.59-36.3374.10.03915.434638350.0220.03926.594.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→36.337 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 1322 5.08 %random
Rwork0.1878 24714 --
obs0.1905 26036 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.14 Å2 / Biso mean: 74.8187 Å2 / Biso min: 35.34 Å2
Refinement stepCycle: final / Resolution: 2.4→36.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 75 66 4124
Biso mean--102.51 57.9 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074163
X-RAY DIFFRACTIONf_angle_d1.0765660
X-RAY DIFFRACTIONf_chiral_restr0.043664
X-RAY DIFFRACTIONf_plane_restr0.005719
X-RAY DIFFRACTIONf_dihedral_angle_d13.2151494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2154X-RAY DIFFRACTION9.925TORSIONAL
12B2154X-RAY DIFFRACTION9.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.49610.31021510.256427182869100
2.4961-2.60970.3461500.241227132863100
2.6097-2.74720.25641510.225527292880100
2.7472-2.91930.3151370.217627382875100
2.9193-3.14450.31891270.240827462873100
3.1445-3.46080.30251430.215827722915100
3.4608-3.9610.24621440.172227552899100
3.961-4.98840.19371630.150827472910100
4.9884-36.34080.19871560.17282796295299
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)
13.1872-0.2168-1.34532.196-1.2097.0739-0.1888-0.3609-0.11520.21710.4480.4378-0.1482-0.6312-0.23970.39810.1084-0.00260.60560.08710.46390.6967-6.002213.7797
24.8854.00056.87976.40515.69869.74070.05682.13730.49430.2480.1560.4193-0.5918-0.0002-0.06890.59-0.05320.02510.78140.01220.442311.32775.2232-3.8404
38.07462.32414.99976.43691.23917.1686-0.51130.71910.7502-0.29810.16130.0046-1.87350.85880.24221.5667-0.45220.13440.86250.03540.774719.47116.8230.5109
44.19933.958-5.57435.7626-4.16058.3553-0.22340.06030.8841-0.0620.42840.3935-0.96530.1651-0.23050.74510.0897-0.12130.71330.01590.499312.29819.274317.4346
52.51961.0898-1.7342.3576-0.79516.7045-0.2656-0.3663-0.22350.02740.1067-0.3082-0.23280.87620.1670.44270.0984-0.0130.58350.04110.407216.57060.904915.539
62.18871.3569-0.05051.6544-0.64146.8008-0.2033-0.6721-0.25470.350.2227-0.29890.34990.73050.11790.46640.240.02830.63330.14840.49838.7432-7.35425.0928
73.02650.74441.54735.01721.39962.3847-0.1469-0.5361-0.69830.63790.5581-0.09931.2633-0.0974-0.45730.63270.20570.0430.63950.22430.70074.828-16.547323.8766
85.85394.83010.0484.1720.43362.1312-0.0195-0.589-0.87960.3228-0.014-1.38280.31380.82290.16040.52490.1976-0.02890.81060.13830.650522.738-3.247121.5802
97.79414.5899-1.36487.61521.60441.3970.5498-1.3890.40711.2708-0.34140.0441-0.130.7436-0.01640.74430.0447-0.0670.984-0.09530.538521.010112.02525.7967
106.23971.61343.67871.83040.67539.47280.107-0.6295-0.62660.3183-0.001-0.12880.5663-0.5707-0.14540.77210.14470.04360.45180.11860.534322.7705-34.910633.4443
114.36171.05651.68852.220.2043.58860.0372-1.007-0.00630.7696-0.1138-0.1334-0.10191.00870.02340.88510.11220.02731.14110.04460.584841.1082-23.719343.1892
125.22281.132-0.93481.0113-2.01186.73-0.0626-0.1243-0.29160.16860.0389-0.0201-0.35340.1689-0.02870.56130.2060.00940.41780.04010.480131.8793-25.284923.5238
137.9174.825-2.57994.8413-3.692.22970.3-1.0170.52150.5405-0.21220.0779-1.03691.1746-0.11431.281-0.0260.08370.9841-0.06040.512634.9524-16.053646.5613
142.80370.1106-0.22632.2618-1.2645.7573-0.0334-0.2216-0.17710.1143-0.00280.4728-0.1828-0.40150.03990.55560.21330.04550.48720.05550.569420.1105-24.538227.0862
152.77463.3934-1.34974.599-1.61988.38450.5075-0.07130.81790.6327-0.2638-0.153-2.01040.447-0.18860.81750.0447-00.53570.00730.794527.9759-13.34229.8209
165.8934-4.8655-5.42584.51284.65885.1094-0.0883-0.72880.9963-0.31060.67140.7482-2.10661.3551-0.61731.2284-0.04710.06560.95640.02980.718850.8396-17.447231.7603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 238 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 251 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 276 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 302 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 303 through 377 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 402 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 403 through 430 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 431 through 459 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 460 through 477 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 237 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 238 through 302 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 303 through 333 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 334 through 364 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 430 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 431 through 459 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 460 through 477 )B0

+
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