[English] 日本語
Yorodumi- PDB-3alo: Crystal structure of human non-phosphorylated MKK4 kinase domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3alo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human non-phosphorylated MKK4 kinase domain ternary complex with AMP-PNP and p38 peptide | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / KINASE / ALLOSTERIC BINDING / ACTIVATION HELIX | ||||||
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: 2.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3alo.cif.gz | 134.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3alo.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 3alo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3alo_validation.pdf.gz | 786.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3alo_full_validation.pdf.gz | 793.2 KB | Display | |
Data in XML | 3alo_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3alo_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/3alo ftp://data.pdbj.org/pub/pdb/validation_reports/al/3alo | HTTPS FTP |
-Related structure data
Related structure data | 3alnSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37470.996 Da / Num. of mol.: 1 / 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: Protein/peptide | Mass: 980.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ANP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Iidazole-HCl pH6.5, 22% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2009 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.85 Å / Num. all: 10566 / Num. obs: 9816 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.66 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.66 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.7 / % possible all: 97.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ALN Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.871 / SU B: 26.686 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.233 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -18.1753 Å / Origin y: -20.3937 Å / Origin z: 11.58 Å
|