+Open data
-Basic information
Entry | Database: PDB / ID: 4ka3 | ||||||
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Title | Structure of MAP kinase in complex with a docking peptide | ||||||
Components |
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Keywords | TRANSFERASE/PROTEIN BINDING / kinase domain / phosphorylation / KIM / TRANSFERASE-PROTEIN BINDING complex | ||||||
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: 2.707 Å | ||||||
Authors | Xin, F.J. / Wu, J.W. | ||||||
Citation | Journal: Sci China Life Sci / Year: 2013 Title: Crystal structure of the p38 alpha MAP kinase in complex with a docking peptide from TAB1 Authors: Xin, F.J. / Wu, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ka3.cif.gz | 152.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ka3.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ka3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ka3_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 4ka3_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 4ka3_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4ka3_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/4ka3 ftp://data.pdbj.org/pub/pdb/validation_reports/ka/4ka3 | HTTPS FTP |
-Related structure data
Related structure data | 1lezS 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: 41338.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P47811, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 3168.479 Da / Num. of mol.: 1 / Fragment: UNP residues 395-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAB1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15750 |
#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: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.86 Details: 100mM Hepes, 22% polyacrylic acid 5100, pH 7.86, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979413 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979413 Å / Relative weight: 1 |
Reflection | Resolution: 2.707→50 Å / Num. all: 13030 / Num. obs: 13001 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 61.93 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.71→2.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.9 / Num. unique all: 662 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LEZ Resolution: 2.707→26.827 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.79 / SU ML: 0.44 / σ(F): 1.34 / Phase error: 26.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.625 Å2 / ksol: 0.313 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.07 Å2 / Biso mean: 70.358 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: LAST / Resolution: 2.707→26.827 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: 5
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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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