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Yorodumi- PDB-2y8q: Structure of the regulatory fragment of mammalian AMPK in complex... -
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-Basic information
Entry | Database: PDB / ID: 2y8q | ||||||
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Title | Structure of the regulatory fragment of mammalian AMPK in complex with one ADP | ||||||
Components |
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Keywords | TRANSFERASE / ADP / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly ...eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / positive regulation of fatty acid oxidation / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / regulation of vesicle-mediated transport / cellular response to organonitrogen compound / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / negative regulation of hepatocyte apoptotic process / tau-protein kinase / bile acid and bile salt transport / protein kinase regulator activity / cellular response to ethanol / protein localization to lipid droplet / negative regulation of TOR signaling / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / negative regulation of tubulin deacetylation / AMP-activated protein kinase activity / Macroautophagy / positive regulation of protein localization / tau-protein kinase activity / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / cellular response to nutrient levels / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to glucose starvation / positive regulation of autophagy / energy homeostasis / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / response to UV / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / negative regulation of insulin receptor signaling pathway / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of glucose import / TP53 Regulates Metabolic Genes / response to gamma radiation / cellular response to glucose stimulus / response to hydrogen peroxide / regulation of circadian rhythm / ADP binding / fatty acid biosynthetic process / autophagy / Wnt signaling pathway / cellular response to hydrogen peroxide / neuron cellular homeostasis / response to estrogen / cellular response to prostaglandin E stimulus / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / response to xenobiotic stimulus / apical plasma membrane / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. ...Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. / Carling, D. / Gamblin, S.J. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Structure of Mammalian Ampk and its Regulation by Adp Authors: Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. ...Authors: Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. / Carling, D. / Gamblin, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y8q.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y8q.ent.gz | 174.5 KB | Display | PDB format |
PDBx/mmJSON format | 2y8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y8q ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y8q | HTTPS FTP |
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-Related structure data
Related structure data | 2y8lC 2ya3C 4cfhC 2v8qS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19486.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 406-555 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P54645, non-specific serine/threonine protein kinase |
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-5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ... , 2 types, 2 molecules BE
#2: Protein | Mass: 10040.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 187-272 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O43741 |
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#3: Protein | Mass: 37434.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80385 |
-Non-polymers , 3 types, 58 molecules
#4: Chemical | ChemComp-ADP / |
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#5: Chemical | ChemComp-AMP / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | ADENOSINE MONOPHOSPHSequence details | THE DNA SEQUENCE WITH HIS-TAG, MSHHHHHHSGLVPRG AND THE ARTIFACTS, SMA (393-395) AND NSCTVN (545-550) ...THE DNA SEQUENCE WITH HIS-TAG, MSHHHHHHSG | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 62 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 17426 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V8Q Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / SU B: 32.605 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.108 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 68.458 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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