+Open data
-Basic information
Entry | Database: PDB / ID: 2oza | ||||||
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Title | Structure of p38alpha complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN/TRANSFERASE / SERINE/THREONINE KINASE / PROTEIN-PROTEIN COMPLEX / P38A / MK2 / SIGNALING PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases ...macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / DSCAM interactions / p38MAPK events / Activation of the AP-1 family of transcription factors / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / leukotriene metabolic process / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / Synthesis of Leukotrienes (LT) and Eoxins (EX) / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Myogenesis / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / VEGFA-VEGFR2 Pathway / calmodulin-dependent protein kinase activity / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / 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 / response to dietary excess / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / inner ear development / cellular response to lipoteichoic acid / response to muramyl dipeptide / Regulation of HSF1-mediated heat shock response / 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 / regulation of cellular response to heat / skeletal muscle tissue development / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / p38MAPK events / regulation of mRNA stability / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / response to cytokine / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / Regulation of TNFR1 signaling / positive regulation of glucose import / negative regulation of canonical Wnt signaling pathway / response to insulin / bone development / cell morphogenesis / osteoblast differentiation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / MAPK cascade / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / kinase activity / protein phosphatase binding / peptidyl-serine phosphorylation / angiogenesis / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / response to lipopolysaccharide / transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | White, A. / Pargellis, C.A. / Studts, J.M. / Werneburg, B.G. / Farmer II, B.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Molecular basis of MAPK-activated protein kinase 2:p38 assembly Authors: White, A. / Pargellis, C.A. / Studts, J.M. / Werneburg, B.G. / Farmer II, B.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oza.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oza.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/2oza ftp://data.pdbj.org/pub/pdb/validation_reports/oz/2oza | 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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Unit cell |
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Details | The biological assembly is a heterodimer containing one p38alpha and one MK2 molecules |
-Components
#1: Protein | Mass: 40983.469 Da / Num. of mol.: 1 / Fragment: MK2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P49137, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 42099.969 Da / Num. of mol.: 1 / Fragment: P38A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P47811, mitogen-activated protein kinase |
#3: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 5 to 20% PEG 4000, 100mM Na Citrate, 5mM DTT, pH 6.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 29, 2004 / Details: SGX-CAT |
Radiation | Monochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→26.8 Å / Num. all: 23258 / Num. obs: 22784 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.115 / Χ2: 0.9 / Net I/σ(I): 8.8 / Scaling rejects: 19252 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.74 % / Mean I/σ(I) obs: 2.1 / Num. measured all: 12295 / Num. unique all: 1924 / Rsym value: 0.59 / Χ2: 1.07 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→26.8 Å / FOM work R set: 0.721 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 72.691 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→26.8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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Xplor file |
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