[English] 日本語
Yorodumi
- PDB-6an1: Crystal structure of the complex between PPARgamma LBD and the li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6an1
TitleCrystal structure of the complex between PPARgamma LBD and the ligand AM-879
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsNUCLEAR PROTEIN / Nuclear receptor / ligand binding domain
Function / homology
Function and homology information


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 / arachidonic acid binding ...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 / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding 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 / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / transcription coregulator binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / lipid metabolic process / regulation of circadian rhythm / PPARA activates gene expression / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / rhythmic process / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding
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 / Zinc finger, C4 type (two domains) ...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
Chem-BKY / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.687 Å
AuthorsVeras, H. / Figueira, A.C. / le Maire, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/22246-0 Brazil
CitationJournal: Front Endocrinol (Lausanne) / Year: 2018
Title: Screening for PPAR Non-Agonist Ligands Followed by Characterization of a Hit, AM-879, with Additional No-Adipogenic and cdk5-Mediated Phosphorylation Inhibition Properties.
Authors: Ribeiro Filho, H.V. / Bernardi Videira, N. / Bridi, A.V. / Tittanegro, T.H. / Helena Batista, F.A. / de Carvalho Pereira, J.G. / de Oliveira, P.S.L. / Bajgelman, M.C. / Le Maire, A. / Figueira, A.C.M.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)65,6303
Polymers65,2452
Non-polymers3841
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-1 kcal/mol
Surface area24920 Å2
Unit cell
Length a, b, c (Å)93.321, 61.366, 118.450
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 32622.746 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-BKY / 4-({2-[(1,3-dioxo-1,3-dihydro-2H-inden-2-ylidene)methyl]phenoxy}methyl)benzoic acid


Mass: 384.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H16O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.9M tri-sodium citrate, 100mM Hepes, 3.5% 1,2-propanediol, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45862 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45862 Å / Relative weight: 1
ReflectionResolution: 2.69→40.74 Å / Num. obs: 18387 / % possible obs: 99.58 % / Redundancy: 6.54 % / Net I/σ(I): 20.59

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.687→40.744 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 946 5.16 %
Rwork0.2181 --
obs0.2211 18347 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.687→40.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 29 12 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044203
X-RAY DIFFRACTIONf_angle_d0.7515679
X-RAY DIFFRACTIONf_dihedral_angle_d5.563084
X-RAY DIFFRACTIONf_chiral_restr0.043657
X-RAY DIFFRACTIONf_plane_restr0.005781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6873-2.8290.31291390.29092442X-RAY DIFFRACTION99
2.829-3.00620.31661420.27212447X-RAY DIFFRACTION100
3.0062-3.23820.33741380.26762495X-RAY DIFFRACTION100
3.2382-3.56390.28261450.24962472X-RAY DIFFRACTION100
3.5639-4.07920.32321250.21282506X-RAY DIFFRACTION100
4.0792-5.13770.25141420.19552506X-RAY DIFFRACTION100
5.1377-40.74880.23391150.19422533X-RAY DIFFRACTION98
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)
14.33094.604-1.77658.3519-2.11738.18750.3977-0.21570.02250.27780.071-0.3688-1.60070.4712-0.55580.59840.08770.09090.72890.01260.613827.5249-1.684930.0773
23.9102-4.1072-2.60837.22353.87084.35410.2595-0.65820.278-1.1074-0.3956-1.4718-0.55040.5565-0.15641.5416-0.06630.16181.19940.18931.193651.0819-4.632431.451
34.95273.12740.15437.3232-2.63886.2987-0.2408-0.7467-0.4604-0.2914-0.15130.19420.8526-0.97210.42030.64570.09510.08291.18840.15610.6211-4.42120.368320.3519
44.2570.71.52652.4346-0.98575.8065-0.48260.18970.1693-0.06090.36120.1472-0.70770.30720.01450.5482-0.01950.02630.87940.00230.43448.412213.1966-0.4526
55.60643.235-5.31684.587-3.18935.0965-0.270.61731.2032-0.48820.5630.2415-0.4378-0.7965-0.37130.68090-0.13490.87820.10040.707714.450523.030811.7639
62.05130.694-1.90571.4080.72468.4239-0.2205-0.51380.54360.30070.0992-0.3098-0.09261.09370.14570.61410.2151-0.05520.94490.05040.51899.411.302526.9108
74.79670.31930.21346.9333-3.78063.3816-0.5276-0.21890.3030.41580.076-1.0495-0.51530.80620.45470.6776-0.021-0.031.0299-0.0850.584422.373216.3686.1558
82.94890.25420.25852.49880.85735.1557-0.2653-0.7639-0.12160.20910.261-0.37010.26790.59710.05550.44760.1739-0.01650.73180.03730.460413.00214.047520.1531
91.82131.94461.02538.70476.46948.47250.2023-0.8581-0.73211.20940.7924-0.59882.27940.2014-0.61940.65170.18350.00180.85030.1420.57374.7215-5.451323.2657
105.41095.502-0.32535.5843-0.36490.29320.0359-0.9241-0.3986-0.1616-0.3449-1.29970.10250.4540.51180.7260.26870.00020.93060.02180.792222.83888.007921.4782
115.8685.8923-5.98975.9503-5.86376.78060.6761-3.20790.14572.0929-1.7045-0.9654-3.2972.20020.11581.5254-0.20350.08611.71250.03621.127621.697724.760925.0178
122.08120.61173.4277.87360.36056.72530.19130.4591-0.8497-0.1736-0.52050.59951.6054-0.49910.04830.8509-0.07360.02980.77640.02370.745921.2546-26.310927.8354
134.13441.7813.32845.57370.32472.99061.1642-1.6883-0.68420.9376-0.4332-0.05890.61350.3092-0.80.88280.16270.08581.32470.0540.60830.143-16.496949.0274
146.48762.3978-5.33842.7799-2.8324.80660.5028-2.0658-0.5515-0.395-1.1901-1.0347-0.04232.31281.23821.32390.0761-0.14451.65890.04880.868645.9411-9.673150.8565
154.07390.4157-0.2021.22541.18255.43980.0245-0.48650.06810.17570.1776-0.1836-0.31170.638-0.13780.65710.10420.0690.72930.07770.460133.6239-9.207535.5248
165.09820.3660.51034.7402-3.02645.67050.2939-0.0718-0.21890.08930.08250.6992-0.1952-0.7596-0.49560.40190.1371-0.04950.4512-0.01360.531419.1441-15.15224.1351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 431 through 457 )
2X-RAY DIFFRACTION2chain 'B' and (resid 458 through 474 )
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 251 )
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 333 )
7X-RAY DIFFRACTION7chain 'A' and (resid 334 through 364 )
8X-RAY DIFFRACTION8chain 'A' and (resid 365 through 403 )
9X-RAY DIFFRACTION9chain 'A' and (resid 404 through 430 )
10X-RAY DIFFRACTION10chain 'A' and (resid 431 through 459 )
11X-RAY DIFFRACTION11chain 'A' and (resid 460 through 475 )
12X-RAY DIFFRACTION12chain 'B' and (resid 208 through 225 )
13X-RAY DIFFRACTION13chain 'B' and (resid 226 through 251 )
14X-RAY DIFFRACTION14chain 'B' and (resid 252 through 276 )
15X-RAY DIFFRACTION15chain 'B' and (resid 277 through 377 )
16X-RAY DIFFRACTION16chain 'B' and (resid 378 through 430 )

+
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