[English] 日本語
Yorodumi- PDB-3vud: Crystal structure of a cysteine-deficient mutant M1 in MAP kinase JNK1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vud | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a cysteine-deficient mutant M1 in MAP kinase JNK1 | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / MAP kinase / Kinase domain / phosphorylation / ATP Binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of DNA replication origin binding / 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 cell killing / dentate gyrus mossy fiber / JUN phosphorylation / regulation of DNA replication origin binding / 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 / MAP-kinase scaffold activity / negative regulation of JUN kinase activity / protein serine/threonine kinase binding / JUN kinase binding / positive regulation of cyclase activity / histone deacetylase regulator activity / positive regulation of NLRP3 inflammasome complex assembly / DSCAM interactions / 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 / MAP kinase activity / regulation of macroautophagy / mitogen-activated protein kinase / negative regulation of intrinsic apoptotic signaling pathway / stress-activated MAPK cascade / response to mechanical stimulus / response to UV / JNK cascade / vesicle-mediated transport / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of protein metabolic process / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / mitochondrial membrane / negative regulation of protein binding / FCERI mediated MAPK activation / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular response to mechanical stimulus / histone deacetylase binding / rhythmic process / regulation of protein localization / cellular senescence / cellular response to oxidative stress / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptidyl-serine phosphorylation / response to oxidative stress / Oxidative Stress Induced Senescence / protein phosphatase binding / cellular response to lipopolysaccharide / positive regulation of apoptotic process / axon / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / synapse / endoplasmic reticulum membrane / positive regulation of gene expression / regulation of DNA-templated transcription / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vud.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vud.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/3vud ftp://data.pdbj.org/pub/pdb/validation_reports/vu/3vud | HTTPS FTP |
---|
-Related structure data
Related structure data | 3vugC 3vuhC 3vuiC 3vukC 3vulC 3vumC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42701.242 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residues 1-364 / Mutation: C245S 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 |
---|---|
#2: Protein/peptide | Mass: 1345.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQF2 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.95 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2011 |
Radiation | Monochromator: monochromatized CuK radiation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.5→42.52 Å / Num. obs: 8390 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.5→3.63 Å / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→31.73 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.807 / SU B: 31.732 / SU ML: 0.485 / Cross valid method: THROUGHOUT / ESU R Free: 0.634 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.779 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→31.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.59 Å / Total num. of bins used: 20
|