+Open data
-Basic information
Entry | Database: PDB / ID: 5y90 | ||||||
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Title | MAP2K7 mutant -C218S | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
Keywords | TRANSFERASE / protein kinase | ||||||
Function / homology | Function and homology information JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / response to tumor necrosis factor / stress-activated MAPK cascade / response to UV / positive regulation of JUN kinase activity / JNK cascade / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular senescence / response to heat / protein phosphatase binding / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / phosphorylation / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / enzyme binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Kinoshita, T. / Hashimoto, T. / Sogabe, Y. / Matsumoto, T. / Sawa, M. / Fukada, H. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: High-resolution structure discloses the potential for allosteric regulation of mitogen-activated protein kinase kinase 7 Authors: Kinoshita, T. / Hashimoto, T. / Sogabe, Y. / Fukada, H. / Matsumoto, T. / Sawa, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y90.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y90.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 5y90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/5y90 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/5y90 | HTTPS FTP |
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-Related structure data
Related structure data | 5y8uC 5b2lS S: Starting model for refinement 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
#1: Protein | Mass: 36851.641 Da / Num. of mol.: 1 / Fragment: UNP residues 103-419 / Mutation: C218S Source method: isolated from a genetically manipulated source Details: hexahistidine tagged at the C-terminal / Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4 / Production host: Escherichia coli B (bacteria) References: UniProt: O14733, mitogen-activated protein kinase kinase | ||
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#2: Chemical | ChemComp-GOL / #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: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→56.05 Å / Num. obs: 84643 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 60.4 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5b2l Resolution: 1.3→56.05 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.547 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.045 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.699 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→56.05 Å
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Refine LS restraints |
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