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Yorodumi- PDB-1lez: CRYSTAL STRUCTURE OF MAP KINASE P38 COMPLEXED TO THE DOCKING SITE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lez | |||||||||
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Title | CRYSTAL STRUCTURE OF MAP KINASE P38 COMPLEXED TO THE DOCKING SITE ON ITS ACTIVATOR MKK3B | |||||||||
Components |
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Keywords | TRANSFERASE / PROTEIN-PEPTIDE COMPLEX / MAP KINASE / SERINE/THREONINE-PROTEIN KINASE / P38 / MKK3b | |||||||||
Function / homology | Function and homology information cellular response to sorbitol / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / Regulation of MITF-M-dependent genes involved in pigmentation / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 ...cellular response to sorbitol / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / Regulation of MITF-M-dependent genes involved in pigmentation / 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 / mitogen-activated protein kinase kinase / Regulation of TP53 Activity through Phosphorylation / Myogenesis / VEGFA-VEGFR2 Pathway / stress-activated protein kinase signaling cascade / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / cartilage condensation / positive regulation of myoblast fusion / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / D-glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / positive regulation of nitric-oxide synthase biosynthetic process / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to dietary excess / response to muramyl dipeptide / MAP kinase activity / regulation of ossification / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / negative regulation of hippo signaling / mitogen-activated protein kinase / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / positive regulation of cardiac muscle cell proliferation / cardiac muscle contraction / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / striated muscle cell differentiation / regulation of cytokine production / positive regulation of interleukin-12 production / response to muscle stretch / positive regulation of brown fat cell differentiation / bone development / Neutrophil degranulation / positive regulation of erythrocyte differentiation / osteoclast differentiation / DNA damage checkpoint signaling / stem cell differentiation / response to ischemia / positive regulation of D-glucose import / cellular response to ionizing radiation / response to insulin / placenta development / negative regulation of canonical Wnt signaling pathway / 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 / cellular response to tumor necrosis factor / heart development / kinase activity / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein tyrosine kinase activity / angiogenesis / protein phosphatase binding / response to lipopolysaccharide / transcription by RNA polymerase II / positive regulation of MAPK cascade / protein kinase activity / intracellular signal transduction / nuclear speck / inflammatory response / positive regulation of protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / DNA damage response / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Chang, C.-I. / Xu, B.-E. / Akella, R. / Cobb, M.H. / Goldsmith, E.J. | |||||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: Crystal structures of MAP kinase p38 complexed to the docking sites on its nuclear substrate MEF2A and activator MKK3b. Authors: Chang, C.I. / Xu, B.E. / Akella, R. / Cobb, M.H. / Goldsmith, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lez.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lez.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lez_validation.pdf.gz | 371.7 KB | Display | wwPDB validaton report |
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Full document | 1lez_full_validation.pdf.gz | 385.2 KB | Display | |
Data in XML | 1lez_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 1lez_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1lez ftp://data.pdbj.org/pub/pdb/validation_reports/le/1lez | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41338.160 Da / Num. of mol.: 1 / Mutation: M30N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: P38 / Plasmid: PET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P47811, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Protein/peptide | Mass: 2071.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: GenBank: 1778153, UniProt: O09110*PLUS |
#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: 2.78 Å3/Da / Density % sol: 55.73 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7 Details: PEG 8000, calcium acetate, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, temperature 289K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 23, 2000 / Details: Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→60 Å / Num. all: 29691 / Num. obs: 29661 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.24→2.29 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 60 Å / Num. obs: 22380 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→60 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→60 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 60 Å / Num. reflection obs: 21231 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |