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Yorodumi- PDB-2v8q: Crystal structure of the regulatory fragment of mammalian AMPK in... -
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-Basic information
Entry | Database: PDB / ID: 2v8q | ||||||
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Title | Crystal structure of the regulatory fragment of mammalian AMPK in complexes with AMP | ||||||
Components |
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Keywords | TRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / KINASE / MAGNESIUM / CBS DOMAIN | ||||||
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 / [acetyl-CoA carboxylase] 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 / [acetyl-CoA carboxylase] 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 / import into nucleus / positive regulation of fatty acid oxidation / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / cellular response to organonitrogen compound / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / negative regulation of hepatocyte apoptotic process / Carnitine metabolism / tau-protein kinase / bile acid and bile salt transport / nucleotide-activated protein kinase complex / cellular response to ethanol / protein localization to lipid droplet / 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 / Macroautophagy / AMP-activated protein kinase activity / positive regulation of protein localization / tau-protein kinase activity / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / cellular response to nutrient levels / fatty acid homeostasis / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / positive regulation of autophagy / negative regulation of lipid catabolic process / regulation of microtubule cytoskeleton organization / energy homeostasis / response to UV / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ADP binding / cellular response to glucose stimulus / response to gamma radiation / TP53 Regulates Metabolic Genes / positive regulation of glucose import / response to hydrogen peroxide / regulation of circadian rhythm / cellular response to hydrogen peroxide / Wnt signaling pathway / autophagy / neuron cellular homeostasis / cellular response to prostaglandin E stimulus / response to estrogen / fatty acid biosynthetic process / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / 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 / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. ...Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / Martin, S.R. / Carling, D. / Gamblin, S.J. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Structural Basis for AMP Binding to Mammalian AMP-Activated Protein Kinase Authors: Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / 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 | 2v8q.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v8q.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v8q ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v8q | HTTPS FTP |
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-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: 17635.799 Da / Num. of mol.: 1 / Fragment: RESIDUES 396-548 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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#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 | ||||
#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 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG ...THE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG CLEAVAGE THE FIRST RESIDUES (M) OF THE SEQUENCE OF CHAIN B IS GENERATED BY THE WAY IT WAS CLONED INTO THE VECTOR | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 42012 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.644 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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