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Yorodumi- PDB-5nzz: Crystal structure of phosphorylated p38aMAPK in complex with TAB1 -
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-Basic information
Entry | Database: PDB / ID: 5nzz | ||||||
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Title | Crystal structure of phosphorylated p38aMAPK in complex with TAB1 | ||||||
Components |
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Keywords | TRANSFERASE / MAPK activated phosphorylated P38 regulation | ||||||
Function / homology | Function and homology information 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 ...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 / protein serine/threonine phosphatase activity / cartilage condensation / cellular response to UV-B / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / non-canonical NF-kappaB signal transduction / fatty acid oxidation / cellular response to lipoteichoic acid / response to dietary excess / response to muramyl dipeptide / enzyme activator activity / regulation of ossification / MAP kinase activity / 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 / heart morphogenesis / skeletal muscle tissue development / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / striated muscle cell differentiation / response to muscle stretch / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of brown fat cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / protein serine/threonine kinase activator activity / osteoclast differentiation / transforming growth factor beta receptor signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of erythrocyte differentiation / placenta development / 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 / response to insulin / NOD1/2 Signaling Pathway / bone development / cell morphogenesis / positive regulation of protein serine/threonine kinase activity / negative regulation of canonical Wnt signaling pathway / CLEC7A (Dectin-1) signaling / cellular response to virus / osteoblast differentiation / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / positive regulation of protein import into nucleus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / cellular response to tumor necrosis factor / kinase activity / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / in utero embryonic development / cellular response to lipopolysaccharide / response to lipopolysaccharide / transcription by RNA polymerase II / positive regulation of MAPK cascade Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å | ||||||
Authors | Nichols, C.E. / De Nicola, G.F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: JCI Insight / Year: 2018 Title: The TAB1-p38 alpha complex aggravates myocardial injury and can be targeted by small molecules. Authors: De Nicola, G.F. / Bassi, R. / Nichols, C. / Fernandez-Caggiano, M. / Golforoush, P.A. / Thapa, D. / Anderson, R. / Martin, E.D. / Verma, S. / Kleinjung, J. / Laing, A. / Hutchinson, J.P. / ...Authors: De Nicola, G.F. / Bassi, R. / Nichols, C. / Fernandez-Caggiano, M. / Golforoush, P.A. / Thapa, D. / Anderson, R. / Martin, E.D. / Verma, S. / Kleinjung, J. / Laing, A. / Hutchinson, J.P. / Eaton, P. / Clark, J. / 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 | 5nzz.cif.gz | 553.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nzz.ent.gz | 460.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/5nzz ftp://data.pdbj.org/pub/pdb/validation_reports/nz/5nzz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 54699.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAB1, MAP3K7IP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15750 #2: Protein | Mass: 41498.121 Da / Num. of mol.: 4 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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-Non-polymers , 4 types, 58 molecules
#3: Chemical | ChemComp-NI / #4: Chemical | ChemComp-AGS / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG3350, 0.1M magensium chloride, 0.1M magnesium sulphate, 0.1M Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→140.36 Å / Num. obs: 109491 / % possible obs: 91.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 51.1 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.084 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5166 / CC1/2: 0.413 / Rpim(I) all: 0.637 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.6→140.359 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.24 / Phase error: 27.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.1 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→140.359 Å
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Refine LS restraints |
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