[English] 日本語
Yorodumi
- PDB-4bcr: Structure of PPARalpha in complex with WY14643 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bcr
TitleStructure of PPARalpha in complex with WY14643
ComponentsPEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / PPAR / FIBRATE
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / nitric oxide metabolic process / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / MDM2/MDM4 family protein binding / positive regulation of lipid biosynthetic process / negative regulation of signaling receptor activity / negative regulation of reactive oxygen species biosynthetic process / positive regulation of gluconeogenesis / RORA activates gene expression / cellular response to starvation / negative regulation of blood pressure / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / fatty acid metabolic process / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / gluconeogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / SUMOylation of intracellular receptors / Heme signaling / wound healing / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / nuclear receptor activity / Circadian Clock / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / lipid binding / chromatin / protein-containing complex binding / positive regulation of DNA-templated transcription / 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 alpha / 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 ...Peroxisome proliferator-activated receptor alpha / 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-WY1 / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsBernardes, A. / Muniz, J.R.C. / Polikarpov, I.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Molecular Mechanism of Peroxisome Proliferator-Activated Receptor Alpha Activation by Wy14643: A New Mode of Ligand Recognition and Receptor Stabilization
Authors: Bernardes, A. / T Souza, P.C. / Muniz, J.R.C. / Ricci, C.G. / Ayers, S.D. / Parekh, N.M. / Godoy, A.S. / Trivella, D.B.B. / Reinach, P. / Webb, P. / Skaf, M.S. / Polikarpov, I.
History
DepositionOct 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4528
Polymers62,0322
Non-polymers1,4196
Water1,11762
1
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7264
Polymers31,0161
Non-polymers7103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7264
Polymers31,0161
Non-polymers7103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.061, 62.359, 180.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0414, 0.9967, 0.0695), (0.9889, 0.0309, 0.1451), (0.1425, 0.0747, -0.987)
Vector: -12.9229, 8.2481, 49.2071)

-
Components

#1: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA / PPARALPHA LBD / PPAR-ALPHA / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP


Mass: 31016.131 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 195-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07869, histone acetyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-WY1 / 2-({4-CHLORO-6-[(2,3-DIMETHYLPHENYL)AMINO]PYRIMIDIN-2-YL}SULFANYL)ACETIC ACID / Pirinixic acid


Mass: 323.798 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H14ClN3O2S / Comment: agonist*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-({4-CHLORO-6-[(2, 3-DIMETHYLPHENYL)AMINO]PYRIMIDIN-2-YL}SULFANYL)ACETIC ACID

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.92 % / Description: NONE
Crystal growDetails: 100 MM TRIS-HCL PH 7.5, 25% PEG 20 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0.39
ReflectionResolution: 2.51→36.56 Å / Num. obs: 22365 / % possible obs: 89.9 % / Observed criterion σ(I): 2.1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 2.51→2.65 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.497→35.479 Å / σ(F): 1.35 / Phase error: 32.14 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2157 1164 5.2 %
Rwork0.1731 --
obs0.174 22321 89.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3
Refinement stepCycle: LAST / Resolution: 2.497→35.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 92 62 4228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114262
X-RAY DIFFRACTIONf_angle_d1.355766
X-RAY DIFFRACTIONf_dihedral_angle_d14.6251566
X-RAY DIFFRACTIONf_chiral_restr0.084665
X-RAY DIFFRACTIONf_plane_restr0.006734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4988-2.61210.38071550.31362758X-RAY DIFFRACTION90
2.6121-2.74930.33921080.282005X-RAY DIFFRACTION66
2.7493-2.92070.27471660.25262900X-RAY DIFFRACTION94
2.9207-3.14480.2851740.23352897X-RAY DIFFRACTION94
3.1448-3.45870.23161160.20022561X-RAY DIFFRACTION82
3.4587-3.95350.21081030.16212078X-RAY DIFFRACTION67
3.9535-4.95930.15661580.11592937X-RAY DIFFRACTION93
4.9593-16.71650.16071500.12382971X-RAY DIFFRACTION90
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)
15.9944-1.5783.49982.8895-3.67538.8829-0.01930.2682-0.7274-0.7003-0.19060.15161.116-0.18430.07570.38510.0275-0.02570.2525-0.07650.3686-21.1396-19.4368-2.6578
23.7012-1.647-5.4664.79060.47019.4740.65360.52450.7593-0.3622-0.26450.2229-0.7327-0.4391-0.37550.4379-0.0096-0.03880.37040.12940.3784-23.13163.2169-12.6188
32.6483-0.8370.50181.52880.36432.546-0.11830.01990.33670.1294-0.0343-0.1629-0.13410.0240.12960.2556-0.02920.00620.18010.00610.2925-13.012-6.21731.2027
42.5104-0.41931.30944.98931.82626.142-0.1321-0.1801-0.21930.2683-0.02510.1450.43530.3990.0780.22110.0197-0.01420.26130.10150.3504-7.5855-24.225311.167
53.4359-0.2275-0.42694.25160.14352.52630.112-0.27960.57910.0045-0.1401-0.6004-0.56190.11580.04710.3696-0.0117-0.06230.28980.04930.3039-5.9032-4.27617.1695
64.5842-4.69911.94525.8469-4.25065.6630.7299-0.5105-1.3507-0.73720.22472.16970.9309-1.0732-0.89520.5059-0.0668-0.08670.30170.03480.719-45.7459-7.85630.2903
70.18710.34560.51741.40451.17623.26660.2531-0.048-0.44280.33510.114-0.15770.78880.4428-0.34840.55530.1184-0.090.2745-0.030.4404-21.0611-13.590754.284
81.8738-0.46230.7690.2332-0.89583.7227-0.00870.05080.06550.00620.0122-0.24770.19770.0919-0.01220.36890.0034-0.00560.1339-0.01820.3507-21.8355-3.656844.8221
94.3858-1.6830.76281.9453-1.0011.84010.05690.16670.2578-0.1601-0.005-0.0409-0.10810.0873-0.03550.3973-0.0190.00610.1431-0.01520.3315-29.32232.286836.3555
105.9181-2.64181.19425.89092.41458.1698-0.15311.44120.9508-0.44280.6635-0.3563-0.94510.8552-0.50010.2905-0.106-0.04610.64690.1460.7193-13.52011.719933.0318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 205:238)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 239:261)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 262:367)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 368:421)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 422:466)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 197:212)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 213:265)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 266:368)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 369:462)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 463:467)

+
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