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Yorodumi- PDB-5o90: Crystal structure of a P38alpha T185G mutant in complex with TAB1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o90 | ||||||
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Title | Crystal structure of a P38alpha T185G mutant in complex with TAB1 peptide. | ||||||
Components |
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Keywords | TRANSFERASE / MAPK14 TRANSFERASE TAB1 | ||||||
Function / homology | Function and homology information positive regulation of cGAS/STING signaling pathway / cardiac septum development / 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 ...positive regulation of cGAS/STING signaling pathway / cardiac septum development / 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 / Regulation of TP53 Activity through Phosphorylation / Myogenesis / coronary vasculature development / VEGFA-VEGFR2 Pathway / aorta development / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / cellular response to UV-B / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / non-canonical NF-kappaB signal transduction / 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 / 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 / heart morphogenesis / stress-activated MAPK cascade / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / striated muscle cell differentiation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / response to muscle stretch / positive regulation of interleukin-12 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of brown fat cell differentiation / Neutrophil degranulation / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / osteoclast differentiation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of erythrocyte differentiation / TNFR1-induced NF-kappa-B signaling pathway / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / lung development / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / placenta development / positive regulation of protein serine/threonine kinase activity / cell morphogenesis / cellular response to virus / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / positive regulation of protein import into nucleus / Interleukin-1 signaling / osteoblast differentiation / glucose metabolic process / 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 / in utero embryonic development / transcription by RNA polymerase II / response to lipopolysaccharide / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Nichols, C.E. / De Nicola, G.F. / Thapa, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol. Cell. Biol. / Year: 2018 Title: TAB1-Induced Autoactivation of p38 alpha Mitogen-Activated Protein Kinase Is Crucially Dependent on Threonine 185. Authors: Thapa, D. / Nichols, C. / Bassi, R. / Martin, E.D. / Verma, S. / Conte, M.R. / De Santis, V. / De Nicola, G.F. / Marber, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o90.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o90.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o90_validation.pdf.gz | 753.7 KB | Display | wwPDB validaton report |
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Full document | 5o90_full_validation.pdf.gz | 760 KB | Display | |
Data in XML | 5o90_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5o90_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/5o90 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o90 | HTTPS FTP |
-Related structure data
Related structure data | 4looS 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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Unit cell |
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-Components
#1: Protein | Mass: 41294.109 Da / Num. of mol.: 1 / Mutation: T185G 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) / Variant (production host): Rosetta 2 References: UniProt: P47811, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 3102.515 Da / Num. of mol.: 1 / Fragment: UNP residues 386-414 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15750 |
#3: Chemical | ChemComp-SB4 / |
#4: 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: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG3350 0.2M Na/K Tartrate 0.1M pH7.0 Bis-Tris Propane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→58.96 Å / Num. obs: 18410 / % possible obs: 99.5 % / Redundancy: 9.4 % / Biso Wilson estimate: 67.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.26→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1340 / CC1/2: 0.651 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LOO Resolution: 2.49→58.959 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 39.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→58.959 Å
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Refine LS restraints |
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LS refinement shell |
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