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- PDB-3mh2: Mutagenesis of p38 MAP kinase establishes key roles of Phe169 in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mh2 | |||||||||
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Title | Mutagenesis of p38 MAP kinase establishes key roles of Phe169 in function and structural dynamics and reveals a novel DFG-out state | |||||||||
![]() | Mitogen-activated protein kinase 14 | |||||||||
![]() | TRANSFERASE / signaling protein | |||||||||
Function / homology | ![]() positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation ...positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation / DSCAM interactions / cellular response to UV-B / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / glucose import / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to dietary excess / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / signal transduction in response to DNA damage / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of interleukin-12 production / positive regulation of brown fat cell differentiation / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / placenta development / cell morphogenesis / platelet activation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / chemotaxis / positive regulation of reactive oxygen species metabolic process / cellular senescence / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / protein phosphatase binding / angiogenesis / Oxidative Stress Induced Senescence / secretory granule lumen / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Namboodiri, H.V. / Karpusas, M. / Bukhtiyarova, M. / Springman, E.B. | |||||||||
![]() | ![]() Title: Mutagenesis of p38alpha MAP kinase establishes key roles of Phe169 in function and structural dynamics and reveals a novel DFG-OUT state. Authors: Bukhtiyarova, M. / Karpusas, M. / Northrop, K. / Namboodiri, H.V. / Springman, E.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.7 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626.5 KB | Display | ![]() |
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Full document | ![]() | 636.6 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mgyC ![]() 3mh0C ![]() 3mh1C ![]() 3mh3C ![]() 1zyjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41359.195 Da / Num. of mol.: 1 / Mutation: F169Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16539, mitogen-activated protein kinase |
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#2: Sugar | ChemComp-BOG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10-20% PEG 4000, 0.1 M cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2004 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 16649 / % possible obs: 96.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Rsym value: 0.049 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.3→2.48 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3334 / Rsym value: 0.283 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZYJ Resolution: 2.3→25.07 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.871 / SU B: 10.435 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.514 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.074 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.303→2.363 Å / Total num. of bins used: 20
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