[English] 日本語
Yorodumi- PDB-4rew: Crystal structure of the non-phosphorylated human alpha1 beta2 ga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rew | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the non-phosphorylated human alpha1 beta2 gamma1 holo-AMPK complex | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / human alpha1 beta2 gamma1 holo-AMPK complex / serine/threonine protein kinase / Axin / CaMKKbeta / LKB1 / glycogen / phosphorylation | ||||||
Function / homology | Function and homology information 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 / 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 / regulation of glycolytic process / positive regulation of protein targeting to mitochondrion / cAMP-dependent protein kinase activity / 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 / positive regulation of protein kinase activity / 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 / 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 / TP53 Regulates Metabolic Genes / response to gamma radiation / cellular response to glucose stimulus / tau protein binding / 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 / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / response to hypoxia / 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 / chromatin Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.58 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Cell Res. / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rew.cif.gz | 347.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rew.ent.gz | 282.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/4rew ftp://data.pdbj.org/pub/pdb/validation_reports/re/4rew | HTTPS FTP |
---|
-Related structure data
Related structure data | 4redC 4rerC 2y94 C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | human alpha1 beta2 gamma1 heterotrimeric complex |
-Components
#1: Protein | Mass: 61486.152 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.) Homo sapiens (human) / Gene: AMPK1, human holo-AMPK alpha1 subunit, PRKAA1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase |
---|---|
#2: Protein | Mass: 22369.527 Da / Num. of mol.: 1 / Fragment: Human AMPK beta2 subunit [A76-I272] Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: human holo-AMPK beta2 subunit, PRKAB2 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43741 |
#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.) Homo sapiens (human) / Gene: human holo-AMPK gamma1 subunit, PRKAG1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54619 |
#4: Chemical | ChemComp-STU / |
#5: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.78 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 6.8 Details: 0.1 M N-acetamido-iminodiacetic acid, pH 6.8, 9% 2-methyl-2,4-pentanediol, and 11.5 mM C-HEGA, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2012 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 4.6→30 Å / Num. obs: 10287 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 20 |
Reflection shell | Resolution: 4.6→4.68 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y94 2y94 Resolution: 4.58→29.01 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 31 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.58→29.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|