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Yorodumi- PDB-3v3v: Structural and functional analysis of quercetagetin, a natural JN... -
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-Basic information
Entry | Database: PDB / ID: 3v3v | ||||||
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Title | Structural and functional analysis of quercetagetin, a natural JNK1 inhibitor | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / PHOSPHORYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dentate gyrus mossy fiber / positive regulation of cell killing / JUN phosphorylation / regulation of CD8-positive, alpha-beta T cell proliferation / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping ...dentate gyrus mossy fiber / positive regulation of cell killing / JUN phosphorylation / regulation of CD8-positive, alpha-beta T cell proliferation / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / negative regulation of JNK cascade / JUN kinase binding / mitogen-activated protein kinase kinase kinase binding / regulation of JNK cascade / positive regulation of cyclase activity / histone deacetylase regulator activity / mitogen-activated protein kinase kinase binding / positive regulation of NLRP3 inflammasome complex assembly / NRAGE signals death through JNK / Activation of the AP-1 family of transcription factors / dendritic growth cone / kinesin binding / Fc-epsilon receptor signaling pathway / cellular response to cadmium ion / mitogen-activated protein kinase / regulation of macroautophagy / axonal growth cone / negative regulation of intrinsic apoptotic signaling pathway / response to UV / stress-activated MAPK cascade / response to mechanical stimulus / protein serine/threonine kinase binding / energy homeostasis / JNK cascade / vesicle-mediated transport / positive regulation of protein metabolic process / NRIF signals cell death from the nucleus / cellular response to amino acid starvation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / regulation of circadian rhythm / FCERI mediated MAPK activation / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / cellular response to reactive oxygen species / cellular response to mechanical stimulus / mitochondrial membrane / cellular senescence / histone deacetylase binding / rhythmic process / regulation of protein localization / Signaling by ALK fusions and activated point mutants / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptidyl-serine phosphorylation / cellular response to oxidative stress / protein phosphatase binding / cellular response to lipopolysaccharide / Oxidative Stress Induced Senescence / response to oxidative stress / neuron projection / positive regulation of apoptotic process / protein phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / synapse / dendrite / endoplasmic reticulum membrane / positive regulation of gene expression / negative regulation of apoptotic process / regulation of DNA-templated transcription / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Baek, S. / Kang, N.J. / Popowicz, G.M. / Arciniega, M. / Jung, S.K. / Byun, S. / Song, N.R. / Heo, Y.S. / Kim, B.Y. / Lee, H.J. ...Baek, S. / Kang, N.J. / Popowicz, G.M. / Arciniega, M. / Jung, S.K. / Byun, S. / Song, N.R. / Heo, Y.S. / Kim, B.Y. / Lee, H.J. / Holak, T.A. / Augustin, M. / Bode, A.M. / Huber, R. / Dong, Z. / Lee, K.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structural and Functional Analysis of the Natural JNK1 Inhibitor Quercetagetin. Authors: Baek, S. / Kang, N.J. / Popowicz, G.M. / Arciniega, M. / Jung, S.K. / Byun, S. / Song, N.R. / Heo, Y.S. / Kim, B.Y. / Lee, H.J. / Holak, T.A. / Augustin, M. / Bode, A.M. / Huber, R. / Dong, Z. / Lee, K.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v3v.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v3v.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 3v3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v3v_validation.pdf.gz | 718.6 KB | Display | wwPDB validaton report |
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Full document | 3v3v_full_validation.pdf.gz | 727.5 KB | Display | |
Data in XML | 3v3v_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 3v3v_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/3v3v ftp://data.pdbj.org/pub/pdb/validation_reports/v3/3v3v | HTTPS FTP |
-Related structure data
Related structure data | 1ukhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 43666.426 Da / Num. of mol.: 1 / Fragment: UNP residues 1-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45983, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 1345.612 Da / Num. of mol.: 1 / Fragment: UNP residues 153-163 / Source method: obtained synthetically / Details: FMOC synthesis / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9WVI9 |
-Non-polymers , 4 types, 36 molecules
#3: Chemical | ChemComp-MYU / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE SEQUENCE MATCHES TO UNP ENTRY P45983-4(ISOFORM 4). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.35 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2.1M Ammonium Sulfate 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2011 / Details: monochromator and mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 18111 / Num. obs: 13950 / % possible obs: 77 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 2.98 / % possible all: 43.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UKH Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 16.648 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.961 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.572 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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