[English] 日本語
Yorodumi- PDB-7z9t: Crystal structure of p38alpha C162S in complex with ATPgS and CAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z9t | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of p38alpha C162S in complex with ATPgS and CAS 2094667-81-7 (in catalytic site, Y35 out), P 1 21 1 | |||||||||
Components | Mitogen-activated protein kinase 14 | |||||||||
Keywords | ONCOPROTEIN / kinase / enzyme / inhibitor / ligand | |||||||||
Function / homology | Function and homology information p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / Regulation of MITF-M-dependent genes involved in pigmentation / 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 ...p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / Regulation of MITF-M-dependent genes involved in pigmentation / 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 / Regulation of TP53 Activity through Phosphorylation / Myogenesis / VEGFA-VEGFR2 Pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / D-glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / response to dietary excess / response to muramyl dipeptide / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / negative regulation of hippo signaling / mitogen-activated protein kinase / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / striated muscle cell differentiation / positive regulation of interleukin-12 production / response to muscle stretch / positive regulation of brown fat cell differentiation / bone development / Neutrophil degranulation / positive regulation of erythrocyte differentiation / osteoclast differentiation / DNA damage checkpoint signaling / stem cell differentiation / positive regulation of D-glucose import / cellular response to ionizing radiation / response to insulin / placenta development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular response to virus / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / cellular response to tumor necrosis factor / kinase activity / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / angiogenesis / protein phosphatase binding / response to lipopolysaccharide / transcription by RNA polymerase II / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / DNA damage response / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Baginski, B. / Pous, J. / Gonzalez, L. / Macias, M.J. / Nebreda, A.R. | |||||||||
Funding support | Spain, 2items
| |||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Characterization of p38 alpha autophosphorylation inhibitors that target the non-canonical activation pathway. Authors: Gonzalez, L. / Diaz, L. / Pous, J. / Baginski, B. / Duran-Corbera, A. / Scarpa, M. / Brun-Heath, I. / Igea, A. / Martin-Malpartida, P. / Ruiz, L. / Pallara, C. / Esguerra, M. / Colizzi, F. / ...Authors: Gonzalez, L. / Diaz, L. / Pous, J. / Baginski, B. / Duran-Corbera, A. / Scarpa, M. / Brun-Heath, I. / Igea, A. / Martin-Malpartida, P. / Ruiz, L. / Pallara, C. / Esguerra, M. / Colizzi, F. / Mayor-Ruiz, C. / Biondi, R.M. / Soliva, R. / Macias, M.J. / Orozco, M. / Nebreda, A.R. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z9t.cif.gz | 372.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z9t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z9t_validation.pdf.gz | 623.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7z9t_full_validation.pdf.gz | 632.7 KB | Display | |
Data in XML | 7z9t_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 7z9t_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/7z9t ftp://data.pdbj.org/pub/pdb/validation_reports/z9/7z9t | HTTPS FTP |
-Related structure data
Related structure data | 7pvuC 7z6iC 4looS 7pv3 7q1a C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41235.020 Da / Num. of mol.: 2 / Mutation: C162S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P47811, mitogen-activated protein kinase #2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 27.5% PEG3350, 0.1M BIS-TRIS pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020 / Details: Elliptically bent mirror |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→79.7 Å / Num. obs: 22113 / % possible obs: 99.2 % / Redundancy: 3 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3207 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LOO Resolution: 2.6→79.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 27.724 / SU ML: 0.288 / Cross valid method: FREE R-VALUE / ESU R Free: 0.347 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.94 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→79.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection: ALL |