[English] 日本語
Yorodumi
- PDB-5azt: Ternary complex of hPPARalpha ligand binding domain, 17-oxoDHA an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5azt
TitleTernary complex of hPPARalpha ligand binding domain, 17-oxoDHA and a SRC1 peptide
Components
  • 15-meric peptide from Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor alpha
KeywordsDNA BINDING PROTEIN / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / LIGAND BINDING DOMAIN / ZINC-FINGER / DNA BINDING / TRANSCRIPTION / OBESITY / NUCLEUS / RECEPTOR / ACTIVATOR / OXIDIZED FATTY ACID / TRANSCRIPTION FACTOR / AGONIST / DUAL AGONIST / COVALENT / PPRE / NUCLEAR / CO-ACTIVATOR
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / negative regulation of cell growth involved in cardiac muscle cell development / regulation of fatty acid metabolic process / negative regulation of appetite / negative regulation of hepatocyte apoptotic process ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / negative regulation of cell growth involved in cardiac muscle cell development / regulation of fatty acid metabolic process / negative regulation of appetite / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / lipoprotein metabolic process / negative regulation of leukocyte cell-cell adhesion / : / 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 / negative regulation of glycolytic process / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of fatty acid metabolic process / DNA-binding transcription activator activity / NFAT protein binding / male mating behavior / hypothalamus development / negative regulation of cholesterol storage / positive regulation of ATP biosynthetic process / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / negative regulation of macrophage derived foam cell differentiation / progesterone receptor signaling pathway / protein-lysine-acetyltransferase activity / epidermis development / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / estrous cycle / positive regulation of lipid biosynthetic process / nuclear retinoid X receptor binding / phosphatase binding / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of blood pressure / : / estrogen receptor signaling pathway / intracellular receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / nitric oxide metabolic process / lactation / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / response to nutrient / MDM2/MDM4 family protein binding / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of gluconeogenesis / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / negative regulation of miRNA transcription / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cerebellum development / cellular response to starvation / nuclear estrogen receptor binding / nuclear receptor binding / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / fatty acid metabolic process / regulation of circadian rhythm / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / mRNA transcription by RNA polymerase II / response to insulin / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / 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 ...Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1 / 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 / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4M5 / Peroxisome proliferator-activated receptor alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.45 Å
AuthorsEgawa, D. / Itoh, T. / Yamamoto, K.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: 17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist
Authors: Egawa, D. / Itoh, T. / Akiyama, Y. / Saito, T. / Yamamoto, K.
History
DepositionOct 23, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 alpha
B: Peroxisome proliferator-activated receptor alpha
C: 15-meric peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2665
Polymers62,5773
Non-polymers6892
Water43224
1
A: Peroxisome proliferator-activated receptor alpha
C: 15-meric peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5573
Polymers32,2132
Non-polymers3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area12770 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7092
Polymers30,3651
Non-polymers3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.460, 59.460, 317.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

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


Mass: 30364.516 Da / Num. of mol.: 2 / Fragment: UNP residues 201-468 / Mutation: F423L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA, NR1C1, PPAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Protein/peptide 15-meric peptide from Nuclear receptor coactivator 1


Mass: 1848.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788
#3: Chemical ChemComp-4M5 / (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid


Mass: 344.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 0.1M HEPES, 35% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→47.61 Å / Num. obs: 8185 / % possible obs: 98.5 % / Redundancy: 10.5 % / Net I/σ(I): 15.6

-
Processing

SoftwareName: REFMAC / Version: 5.8.0103 / Classification: refinement
RefinementResolution: 3.45→11 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.74 / SU B: 40.739 / SU ML: 0.65 / Cross valid method: THROUGHOUT / ESU R Free: 0.823 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30763 400 5.1 %RANDOM
Rwork0.25254 ---
obs0.25537 7408 94.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.093 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0 Å2-0 Å2
2--0.51 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 3.45→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 50 24 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194182
X-RAY DIFFRACTIONr_bond_other_d0.0030.024101
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9845644
X-RAY DIFFRACTIONr_angle_other_deg2.12439412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7775521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65124.943174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14215736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.951516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02920
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2173.1642096
X-RAY DIFFRACTIONr_mcbond_other1.2153.1632095
X-RAY DIFFRACTIONr_mcangle_it2.1054.7352613
X-RAY DIFFRACTIONr_mcangle_other2.1044.7372614
X-RAY DIFFRACTIONr_scbond_it1.5643.2222086
X-RAY DIFFRACTIONr_scbond_other1.5623.222084
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3594.8063031
X-RAY DIFFRACTIONr_long_range_B_refined4.27625.0335065
X-RAY DIFFRACTIONr_long_range_B_other4.27625.0395066
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.45→3.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 18 -
Rwork0.27 476 -
obs--90.81 %

+
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