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Yorodumi- PDB-4loo: Structural basis of autoactivation of p38 alpha induced by TAB1 (... -
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-Basic information
Entry | Database: PDB / ID: 4loo | ||||||
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Title | Structural basis of autoactivation of p38 alpha induced by TAB1 (Monoclinic crystal form) | ||||||
Components |
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Keywords | TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / protein kinase / kinase-regulatory protein complex / MAPK / autoactivation / autophosphorylation | ||||||
Function / homology | Function and homology information IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of cGAS/STING signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / cardiac septum development / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation ...IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of cGAS/STING signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / cardiac septum development / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / 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 / Ub-specific processing proteases / coronary vasculature development / VEGFA-VEGFR2 Pathway / kinase activator activity / 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 / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / Neutrophil degranulation / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / lung development / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / placenta development / 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 / 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 / protein kinase activity / intracellular signal transduction / nuclear speck Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Chaikuad, A. / DeNicola, G.F. / Krojer, T. / Allerston, C.K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Marber, M.S. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Mechanism and consequence of the autoactivation of p38 alpha mitogen-activated protein kinase promoted by TAB1. Authors: De Nicola, G.F. / Martin, E.D. / Chaikuad, A. / Bassi, R. / Clark, J. / Martino, L. / Verma, S. / Sicard, P. / Tata, R. / Atkinson, R.A. / Knapp, S. / Conte, M.R. / 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 | 4loo.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4loo.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 4loo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4loo_validation.pdf.gz | 768.1 KB | Display | wwPDB validaton report |
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Full document | 4loo_full_validation.pdf.gz | 771.2 KB | Display | |
Data in XML | 4loo_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4loo_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/4loo ftp://data.pdbj.org/pub/pdb/validation_reports/lo/4loo | HTTPS FTP |
-Related structure data
Related structure data | 4lopC 4loqC 3queS S: Starting model for refinement C: citing same article (ref.) |
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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: 41395.211 Da / Num. of mol.: 1 / Fragment: kinase domain (1-360) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: MAPK14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli) References: UniProt: P47811, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 3102.515 Da / Num. of mol.: 1 / Fragment: residues 384-412 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8CF89 |
#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: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% medium-molecular weight PEG Smears, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2012 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→59.18 Å / Num. all: 27022 / Num. obs: 27019 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2 / Num. unique all: 3898 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QUE Resolution: 1.95→46.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.841 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.192 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.518 Å2
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Refine analyze | Luzzati coordinate error obs: 0.272 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→46.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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