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Yorodumi- PDB-1lew: CRYSTAL STRUCTURE OF MAP KINASE P38 COMPLEXED TO THE DOCKING SITE... -
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-Basic information
Entry | Database: PDB / ID: 1lew | ||||||
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Title | CRYSTAL STRUCTURE OF MAP KINASE P38 COMPLEXED TO THE DOCKING SITE ON ITS NUCLEAR SUBSTRATE MEF2A | ||||||
Components |
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Keywords | TRANSFERASE / PROTEIN-PEPTIDE COMPLEX / MAP KINASE / SERINE/THREONINE-PROTEIN KINASE / P38 / MEF2A | ||||||
Function / homology | Function and homology information ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / 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 / cardiac conduction ...ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / 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 / cardiac conduction / NOD1/2 Signaling Pathway / ADP signalling through P2Y purinoceptor 1 / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / mitochondrial genome maintenance / Myogenesis / VEGFA-VEGFR2 Pathway / dendrite morphogenesis / muscle organ development / 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 / histone acetyltransferase binding / cellular response to UV-B / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / positive regulation of cardiac muscle hypertrophy / glucose import / negative regulation of hippo signaling / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / SMAD binding / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / striated muscle cell differentiation / response to muscle stretch / cellular response to calcium ion / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / Neutrophil degranulation / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / placenta development / positive regulation of glucose import / stem cell differentiation / cellular response to ionizing radiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cellular response to virus / spindle pole / histone deacetylase binding / 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 / kinase activity / heart development / peptidyl-serine phosphorylation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / DNA-binding transcription factor binding / transcription regulator complex / cellular response to lipopolysaccharide / angiogenesis / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / response to lipopolysaccharide / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein kinase activity / intracellular signal transduction / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
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 | 1lew.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lew.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lew_validation.pdf.gz | 376 KB | Display | wwPDB validaton report |
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Full document | 1lew_full_validation.pdf.gz | 385 KB | Display | |
Data in XML | 1lew_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1lew_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1lew ftp://data.pdbj.org/pub/pdb/validation_reports/le/1lew | 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
#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, Crk1, Csbp1, Csbp2 / Plasmid: PET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P47811, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 1379.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q02078 |
#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: 55.83 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.5 Details: PEG 8000, HEPES, pH 7.5, VAPOR DIFFUSION, temperature 289K | ||||||||||||||||||||||||
Crystal grow | *PLUS 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-BM / Wavelength: 0.9795 Å |
Detector | Type: APS-1 / Detector: CCD / Date: Feb 2, 2001 / 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: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. all: 28374 / Num. obs: 28346 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.26→2.37 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. obs: 22800 / Rmerge(I) obs: 0.13 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection obs: 20610 / Rfactor all: 0.245 / Rfactor obs: 0.235 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.215 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |