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- PDB-4rer: Crystal structure of the phosphorylated human alpha1 beta2 gamma1... -
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Basic information
Entry | Database: PDB / ID: 4rer | |||||||||
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Title | Crystal structure of the phosphorylated human alpha1 beta2 gamma1 holo-AMPK complex bound to AMP and cyclodextrin | |||||||||
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![]() | TRANSFERASE / human alpha1 beta2 gamma1 holo-AMPK complex / serine/threonine protein kinase / axin / CaMKKbeta / LKB1 / glycogen / Phosphorylation | |||||||||
Function / homology | ![]() negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [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 ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [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 skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / 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 / cellular response to ethanol / negative regulation of TOR signaling / protein localization to lipid droplet / protein kinase regulator activity / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / regulation of glycolytic process / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / cAMP-dependent protein kinase activity / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / tau-protein kinase activity / Macroautophagy / positive regulation of protein localization / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / positive regulation of protein kinase activity / fatty acid homeostasis / cellular response to nutrient levels / negative regulation of lipid catabolic process / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / response to UV / energy homeostasis / 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 / response to gamma radiation / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / tau protein binding / regulation of circadian rhythm / ADP binding / Wnt signaling pathway / fatty acid biosynthetic process / autophagy / cellular response to hydrogen peroxide / neuron cellular homeostasis / response to estrogen / cellular response to prostaglandin E stimulus / glucose metabolic process / cellular response to xenobiotic stimulus / rhythmic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / apical plasma membrane / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / chromatin binding / positive regulation of cell population proliferation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhou, X.E. / Ke, J. / Li, X. / Wang, L. / Gu, X. / de Waal, P.W. / Tan, M.H.E. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K. | |||||||||
![]() | ![]() Title: Structural basis of AMPK regulation by adenine nucleotides and glycogen. Authors: Li, X. / Wang, L. / Zhou, X.E. / Ke, J. / de Waal, P.W. / Gu, X. / Tan, M.H. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 415.7 KB | Display | ![]() |
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PDB format | ![]() | 340.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4redC ![]() 4rewC ![]() 2y94 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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Details | The heterotrimeric serine/threonine protein kinase |
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Components
-5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BG
#2: Protein | Mass: 22449.506 Da / Num. of mol.: 1 / Fragment: Human AMPK beta2 subunit [A76-I272] Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 34645.109 Da / Num. of mol.: 1 / Fragment: Human AMPK gamma1 subunit [S24-G327] Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 61566.129 Da / Num. of mol.: 1 / Fragment: Human AMPK alpha1 subunit [G11-Q550] / Mutation: E471G, E474A, K476A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase |
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#4: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin |
-Non-polymers , 3 types, 5 molecules ![](data/chem/img/STU.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/AMP.gif)
#5: Chemical | ChemComp-STU / |
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#6: Chemical | ChemComp-EPE / |
#7: Chemical |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 12% PEG 4000,0.1 M HEPES, pH7.8, 10% 2-propanol (v/v) and 0.19 mM 7-cyclohexyl-1-heptyl-D-maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 4.05→40 Å / Num. all: 16738 / Num. obs: 16621 / % possible obs: 99.3 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 4.05→4.19 Å / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y94 ![]() 2y94 Resolution: 4.047→39.657 Å / SU ML: 0.55 / σ(F): 1.35 / Phase error: 28.23 / Stereochemistry target values: MAXIMUM-LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.047→39.657 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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