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- PDB-2vv4: hPPARgamma Ligand binding domain in complex with 6-oxoOTE -

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Basic information

Entry
Database: PDB / ID: 2vv4
TitlehPPARgamma Ligand binding domain in complex with 6-oxoOTE
Components(PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA) x 2
KeywordsRECEPTOR / NUCLEAR RECEPTOR / LIGAND BINDING DOMAIN / OXIDISED FATTY ACID / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding ...prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / 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 / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / negative regulation of MAPK cascade / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / regulation of blood pressure / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
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 / 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-6OB / Chem-6OC / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsItoh, T. / Fairall, L. / Schwabe, J.W.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural Basis for the Activation of Pparg by Oxidised Fatty Acids
Authors: Itoh, T. / Fairall, L. / Amin, K. / Inaba, Y. / Szanto, A. / Balint, B.L. / Nagy, L. / Yamamoto, K. / Schwabe, J.W.R.
History
DepositionJun 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,5344
Polymers62,9132
Non-polymers6212
Water2,594144
1
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7602
Polymers31,4501
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7742
Polymers31,4641
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.780, 61.580, 118.770
Angle α, β, γ (deg.)90.00, 103.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA / PPAR GAMMA / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3


Mass: 31449.520 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475
Source method: isolated from a genetically manipulated source
Details: 6-OXOOTE / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P37231
#2: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA / PPAR GAMMA / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3


Mass: 31463.547 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475
Source method: isolated from a genetically manipulated source
Details: 6-OXOOTE / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P37231
#3: Chemical ChemComp-6OC / (8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid


Mass: 310.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30O4
#4: Chemical ChemComp-6OB / (8E,10S,12Z)-10-hydroxy-6-oxooctadeca-8,12-dienoic acid


Mass: 310.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details6-OXOOCTADECATRIENOIC ACID (6OC): LIGAND IS COVALENTLY COUPLED AT C8 TO CYS285 IN MONOMER A 6- ...6-OXOOCTADECATRIENOIC ACID (6OC): LIGAND IS COVALENTLY COUPLED AT C8 TO CYS285 IN MONOMER A 6-OXOOCTADECATRIENOIC ACID (6OB): LIGAND IS COVALENTLY COUPLED AT C10 TO CYS285 IN MONOMER B
Sequence detailsRESIDUE NUMBERING CORRESPONDS TO ISOFORM 1

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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: 55.5 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: PH 8, TRIS 100MM, 0.7M NACITRATE, 1MM TCEP, 0.5MM EDTA, VAPOUR DIFFUSION, DARK, UNDER NITROGEN, 22 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.35→51.03 Å / Num. obs: 53512 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.1
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I4P

2i4p


Resolution: 2.35→51.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1765036.14 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2671 5 %RANDOM
Rwork0.226 ---
obs0.226 53512 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5652 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å22.62 Å2
2--12.55 Å20 Å2
3----12.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.35→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 42 144 4187
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 380 4.3 %
Rwork0.294 8463 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION36OC_PA.PARAM6OC_PA.TOP
X-RAY DIFFRACTION46OB_PA.PARAM6OB_PA.TOP

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