[English] 日本語
Yorodumi- PDB-3tg1: Crystal structure of p38alpha in complex with a MAPK docking partner -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tg1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of p38alpha in complex with a MAPK docking partner | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/HYDROLASE / Kinase/Rhodanese-like domain / docking interaction / TRANSFERASE-HYDROLASE complex | ||||||
Function / homology | Function and homology information negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Signaling by MAPK mutants / negative regulation of oligodendrocyte differentiation / Regulation of TP53 Activity through Phosphorylation / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / Myogenesis / negative regulation of JNK cascade / JUN kinase binding / positive regulation of regulatory T cell differentiation / VEGFA-VEGFR2 Pathway / negative regulation of stress-activated MAPK cascade / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / myosin phosphatase activity / cartilage condensation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of hippo signaling / protein-serine/threonine phosphatase / positive regulation of myotube differentiation / NFAT protein binding / oligodendrocyte differentiation / glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / phosphatase activity / fatty acid oxidation / cellular response to lipoteichoic acid / response to dietary excess / response to muramyl dipeptide / negative regulation of respiratory burst involved in inflammatory response / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / dephosphorylation / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / Neutrophil degranulation / negative regulation of cell migration / protein-tyrosine-phosphatase / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / placenta development / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / cellular response to virus / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / Negative regulation of MAPK pathway / glucose metabolic process / negative regulation of epithelial cell proliferation / positive regulation of reactive oxygen species metabolic process / MAPK cascade / kinase activity / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Zhang, Y.Y. / Wu, J.W. / Wang, Z.X. | ||||||
Citation | Journal: Sci.Signal. / Year: 2011 Title: A Distinct Interaction Mode Revealed by the Crystal Structure of the Kinase p38alpha with the MAPK Binding Domain of the Phosphatase MKP5. Authors: Zhang, Y.Y. / Wu, J.W. / Wang, Z.X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tg1.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tg1.ent.gz | 164.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tg1_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tg1_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 3tg1_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3tg1_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/3tg1 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/3tg1 | HTTPS FTP |
-Related structure data
Related structure data | 3tg3C 1p38 2oucS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43509.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P47811, mitogen-activated protein kinase |
---|---|
#2: Protein | Mass: 18074.928 Da / Num. of mol.: 1 / Fragment: KBD (UNP RESIDUES 139-288) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 100mM Tris pH7.5, 9% [w/v] polyethylene glycol 3350, 8% [w/v] sucrose, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2009 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→36.214 Å / Num. obs: 17026 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.58 / Num. unique all: 1565 / % possible all: 93.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P38, 2OUC Resolution: 2.71→36.214 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.34 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.609 Å2 / ksol: 0.337 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→36.214 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
|