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Yorodumi- PDB-3vul: Crystal structure of a cysteine-deficient mutant M1 in MAP kinase JNK1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vul | ||||||
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Title | Crystal structure of a cysteine-deficient mutant M1 in MAP kinase JNK1 | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSCRIPTION / phosphorylation / ATP Binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dentate gyrus mossy fiber / JUN phosphorylation / positive regulation of cell killing / 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 / positive regulation of establishment of protein localization to mitochondrion / JUN kinase activity ...dentate gyrus mossy fiber / JUN phosphorylation / positive regulation of cell killing / 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 / positive regulation of establishment of protein localization to mitochondrion / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / negative regulation of JUN kinase activity / MAP-kinase scaffold activity / JUN kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / NRAGE signals death through JNK / protein kinase inhibitor activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / kinesin binding / regulation of JNK cascade / mitogen-activated protein kinase / regulation of macroautophagy / negative regulation of intrinsic apoptotic signaling pathway / response to UV / protein serine/threonine kinase binding / stress-activated MAPK cascade / response to mechanical stimulus / energy homeostasis / vesicle-mediated transport / JNK cascade / positive regulation of protein metabolic process / cellular response to cadmium ion / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / FCERI mediated MAPK activation / peptidyl-threonine phosphorylation / positive regulation of JNK cascade / mitochondrial membrane / regulation of circadian rhythm / histone deacetylase binding / cellular response to mechanical stimulus / cellular response to reactive oxygen species / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to oxidative stress / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / positive regulation of apoptotic process / protein phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Nakaniwa, T. / Kinoshita, T. / Inoue, T. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Seven cysteine-deficient mutants depict the interplay between thermal and chemical stabilities of individual cysteine residues in mitogen-activated protein kinase c-Jun N-terminal kinase 1 Authors: Nakaniwa, T. / Fukada, H. / Inoue, T. / Gouda, M. / Nakai, R. / Kirii, Y. / Adachi, M. / Tamada, T. / Segawa, S. / Kuroki, R. / Tada, T. / Kinoshita, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vul.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vul.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vul_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 3vul_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 3vul_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 3vul_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/3vul ftp://data.pdbj.org/pub/pdb/validation_reports/vu/3vul | HTTPS FTP |
-Related structure data
Related structure data | 3vudC 3vugC 3vuhC 3vuiC 3vukC 3vumC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42641.078 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residues 1-364 / Mutation: C245S, C116S, C163A, C79V, C137V, C213V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A1L4K2, UniProt: P45983*PLUS, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 1345.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQF2 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.2M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 16976 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→33.78 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.858 / SU B: 15.437 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.582 / ESU R Free: 0.385 / 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: 51.439 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→33.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.805→2.878 Å / Total num. of bins used: 20
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