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Yorodumi- PDB-3aln: Crystal Structure of human non-phosphorylated MKK4 kinase domain ... -
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-Basic information
Entry | Database: PDB / ID: 3aln | ||||||
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Title | Crystal Structure of human non-phosphorylated MKK4 kinase domain complexed with AMP-PNP | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 4 | ||||||
Keywords | TRANSFERASE / KINASE / PROTEIN AMP-PNP COMPLEX | ||||||
Function / homology | Function and homology information smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cellular response to sorbitol / JUN kinase kinase activity / cell growth involved in cardiac muscle cell development / mitogen-activated protein kinase kinase / negative regulation of motor neuron apoptotic process / positive regulation of nitric-oxide synthase biosynthetic process / Fc-epsilon receptor signaling pathway / Uptake and function of anthrax toxins ...smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cellular response to sorbitol / JUN kinase kinase activity / cell growth involved in cardiac muscle cell development / mitogen-activated protein kinase kinase / negative regulation of motor neuron apoptotic process / positive regulation of nitric-oxide synthase biosynthetic process / Fc-epsilon receptor signaling pathway / Uptake and function of anthrax toxins / JNK cascade / dendrite cytoplasm / MAP3K8 (TPL2)-dependent MAPK1/3 activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of DNA replication / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular response to mechanical stimulus / MAPK cascade / cellular senescence / positive regulation of neuron apoptotic process / perikaryon / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / molecular adaptor activity / protein kinase activity / positive regulation of protein phosphorylation / phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Matsumoto, T. / Kinoshita, T. / Kirii, Y. / Yokota, K. / Hamada, K. / Tada, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2010 Title: Crystal structures of MKK4 kinase domain reveal that substrate peptide binds to an allosteric site and induces an auto-inhibition state Authors: Matsumoto, T. / Kinoshita, T. / Kirii, Y. / Yokota, K. / Hamada, K. / Tada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aln.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aln.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 3aln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aln_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3aln_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3aln_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 3aln_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/3aln ftp://data.pdbj.org/pub/pdb/validation_reports/al/3aln | HTTPS FTP |
-Related structure data
Related structure data | 3aloC 3fmeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37470.996 Da / Num. of mol.: 3 / Fragment: PROTEIN KINASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JNKK1, MAP2K4, MEK4, MKK4, PRKMK4, SERK1 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45985, mitogen-activated protein kinase kinase #2: Chemical | #3: Chemical | |
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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: 1.95 Å3/Da / Density % sol: 36.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Imidazole-HCl pH6.5, 22% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→86.56 Å / Num. all: 39879 / Num. obs: 38603 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.54 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.81 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 3.1 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FME Resolution: 2.3→46 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.838 / SU B: 12.405 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.587 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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