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- PDB-7wgl: X-ray structure of human PPAR delta ligand binding domain-bezafib... -

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Basic information

Entry
Database: PDB / ID: 7wgl
TitleX-ray structure of human PPAR delta ligand binding domain-bezafibrate co-crystals obtained by co-crystallization
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR
Function / homology
Function and homology information


keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / positive regulation of epidermis development / axon ensheathment / positive regulation of fat cell proliferation / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration ...keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / positive regulation of epidermis development / axon ensheathment / positive regulation of fat cell proliferation / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration / fatty acid catabolic process / proteoglycan metabolic process / negative regulation of collagen biosynthetic process / positive regulation of myoblast proliferation / positive regulation of fatty acid oxidation / phospholipid biosynthetic process / Carnitine shuttle / negative regulation of myoblast differentiation / response to vitamin A / Signaling by Retinoic Acid / positive regulation of fatty acid metabolic process / fatty acid beta-oxidation / negative regulation of cholesterol storage / cell-substrate adhesion / decidualization / nuclear steroid receptor activity / keratinocyte proliferation / adipose tissue development / NF-kappaB binding / fatty acid transport / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of fat cell differentiation / response to glucose / cholesterol metabolic process / energy homeostasis / intracellular receptor signaling pathway / hormone-mediated signaling pathway / cellular response to nutrient levels / embryo implantation / negative regulation of miRNA transcription / response to activity / generation of precursor metabolites and energy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of smooth muscle cell proliferation / lipid metabolic process / apoptotic signaling pathway / wound healing / fatty acid metabolic process / negative regulation of cell growth / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / vasodilation / transcription coactivator binding / nuclear receptor activity / glucose metabolic process / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / heart development / cellular response to lipopolysaccharide / cellular response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of gene expression / regulation of transcription by RNA polymerase II / lipid binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor, beta / 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 ...Peroxisome proliferator-activated receptor, beta / 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-PEM / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.091 Å
AuthorsKamata, S. / Honda, A. / Machida, Y. / Uchii, K. / Shiiyama, Y. / Masuda, R. / Oyama, T. / Ishii, I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K16359 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101071 Japan
CitationJournal: Int J Mol Sci / Year: 2022
Title: Functional and Structural Insights into Human PPAR alpha / delta / gamma Subtype Selectivity of Bezafibrate, Fenofibric Acid, and Pemafibrate.
Authors: Honda, A. / Kamata, S. / Akahane, M. / Machida, Y. / Uchii, K. / Shiiyama, Y. / Habu, Y. / Miyawaki, S. / Kaneko, C. / Oyama, T. / Ishii, I.
History
DepositionDec 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,3646
Polymers63,0552
Non-polymers1,3084
Water86548
1
A: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1823
Polymers31,5281
Non-polymers6542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-10 kcal/mol
Surface area12610 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1823
Polymers31,5281
Non-polymers6542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-9 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.481, 93.806, 96.232
Angle α, β, γ (deg.)90.000, 97.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator-activated receptor delta / PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member ...PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member 2 / Peroxisome proliferator-activated receptor beta / PPAR-beta


Mass: 31527.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PEM / 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID


Mass: 361.819 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20ClNO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.05 M Bis-tis propane (pH 8.5), 14% PEG8000, 0.1 M KSCN, 6% propanediol, 0.001 M EDTA, 0.001 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2021 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→47.72 Å / Num. obs: 40661 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 16.2 / Num. measured all: 140997 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.150.361331010.9150.2310.4397.6
9.11-47.720.01649.250910.010.01997.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.55 Å47.72 Å
Translation6.55 Å47.72 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575-000refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZNQ

2znq


Resolution: 2.091→37.972 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 3739 4.82 %
Rwork0.1944 73872 -
obs0.1959 40615 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.12 Å2 / Biso mean: 49.5683 Å2 / Biso min: 23.26 Å2
Refinement stepCycle: final / Resolution: 2.091→37.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 184 48 4370
Biso mean--59.93 43.58 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094338
X-RAY DIFFRACTIONf_angle_d0.9635861
X-RAY DIFFRACTIONf_chiral_restr0.053667
X-RAY DIFFRACTIONf_plane_restr0.006732
X-RAY DIFFRACTIONf_dihedral_angle_d17.4962605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.091-2.11720.30671230.2718254891
2.1172-2.1450.31041150.2683271394
2.145-2.17440.27671220.2556275994
2.1744-2.20550.26121640.2528265993
2.2055-2.23840.32591300.2621252789
2.2384-2.27330.32671450.2399254090
2.2733-2.31060.29091420.2389274894
2.3106-2.35040.26671430.2178271897
2.3504-2.39320.27021370.2241273497
2.3932-2.43920.291670.2188276997
2.4392-2.4890.27661450.2093285399
2.489-2.54310.22661650.213272298
2.5431-2.60220.27481270.2081286198
2.6022-2.66730.24621520.2218276898
2.6673-2.73940.25881280.1998280298
2.7394-2.820.31241270.2105284198
2.82-2.9110.28661260.2239276898
2.911-3.0150.27461440.2216279197
3.015-3.13560.23171570.2459273197
3.1356-3.27830.2661640.2216279097
3.2783-3.4510.24511530.2067269097
3.451-3.6670.24591210.1963282697
3.667-3.94990.19081280.1843275195
3.9499-4.34690.18061520.1599250189
4.3469-4.97470.16411140.1529279698
4.9747-6.2630.2051140.1874284999
6.263-37.9720.15081340.1465281798

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