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- PDB-3cwd: Molecular recognition of nitro-fatty acids by PPAR gamma -

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Basic information

Entry
Database: PDB / ID: 3cwd
TitleMolecular recognition of nitro-fatty acids by PPAR gamma
Components
  • Peroxisome proliferator-activated receptor gamma
  • SRC1-2 PEPTIDE
KeywordsTRANSCRIPTION / ppar gamma / nuclear receptor / SRC1-2 motif / Activator / Alternative splicing / Diabetes mellitus / Disease mutation / DNA-binding / Metal-binding / Nucleus / Obesity / Phosphoprotein / Polymorphism / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / positive regulation of female receptivity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / positive regulation of female receptivity / 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 / hypothalamus development / DNA binding domain binding / male mating behavior / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / estrous cycle / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of BMP signaling pathway / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / negative regulation of mitochondrial fission / Synthesis of bile acids and bile salts / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / negative regulation of signaling receptor activity / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cell maturation / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / nuclear estrogen receptor binding / transcription coregulator binding / nuclear receptor binding / hippocampus development / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / Heme signaling / SUMOylation of intracellular receptors / RNA polymerase II transcription regulatory region sequence-specific DNA binding
Similarity search - Function
Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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 ...Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / 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 / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
(9E,12Z)-10-nitrooctadeca-9,12-dienoic acid / (9Z,12E)-12-nitrooctadeca-9,12-dienoic acid / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMartynowski, D. / Li, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Molecular recognition of nitrated fatty acids by PPAR gamma.
Authors: Li, Y. / Zhang, J. / Schopfer, F.J. / Martynowski, D. / Garcia-Barrio, M.T. / Kovach, A. / Suino-Powell, K. / Baker, P.R. / Freeman, B.A. / Chen, Y.E. / Xu, H.E.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: SRC1-2 PEPTIDE
D: SRC1-2 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8488
Polymers65,5464
Non-polymers1,3024
Water4,738263
1
A: Peroxisome proliferator-activated receptor gamma
C: SRC1-2 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4244
Polymers32,7732
Non-polymers6512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area13840 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor gamma
D: SRC1-2 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4244
Polymers32,7732
Non-polymers6512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-8.4 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.043, 86.197, 97.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30867.908 Da / Num. of mol.: 2 / Fragment: PPAR gamma LBD domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37231
#2: Protein/peptide SRC1-2 PEPTIDE


Mass: 1905.186 Da / Num. of mol.: 2 / Fragment: LXXLL motif of SRC1-2 / Source method: obtained synthetically / References: UniProt: Q15788
#3: Chemical ChemComp-LNA / (9E,12Z)-10-nitrooctadeca-9,12-dienoic acid


Mass: 325.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H31NO4
#4: Chemical ChemComp-LNB / (9Z,12E)-12-nitrooctadeca-9,12-dienoic acid


Mass: 325.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H31NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.27 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32973

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.11 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.877 / SU B: 15.708 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29002 1346 4.9 %RANDOM
Rwork0.23296 ---
obs0.23572 25965 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 92 263 4798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224605
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7642.0056178
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1125.073205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94915892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0781521
X-RAY DIFFRACTIONr_chiral_restr0.1120.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023337
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.22274
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23141
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4030.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.52852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33324452
X-RAY DIFFRACTIONr_scbond_it2.0331950
X-RAY DIFFRACTIONr_scangle_it2.9254.51725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 100 -
Rwork0.227 1960 -
obs--100 %

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