+Open data
-Basic information
Entry | Database: PDB / ID: 4eak | ||||||
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Title | Co-crystal structure of an AMPK core with ATP | ||||||
Components |
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Keywords | TRANSFERASE / AMPK | ||||||
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 / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : ...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 / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / 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 / nucleotide-activated protein kinase complex / : / negative regulation of hepatocyte apoptotic process / tau-protein kinase / protein kinase regulator activity / cellular response to ethanol / bile acid and bile salt transport / protein localization to lipid droplet / negative regulation of TOR signaling / bile acid signaling pathway / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / tau-protein kinase activity / positive regulation of protein localization / 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 / 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 / positive regulation of glucose import / response to gamma radiation / cellular response to glucose stimulus / response to hydrogen peroxide / 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 / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / 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 / chromatin binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex binding / chromatin / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / signal transduction Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chen, L. / Wang, J. / Zhang, Y.-Y. / Yan, S.F. / Neumann, D. / Schlattner, U. / Wang, Z.-X. / Wu, J.-W. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: AMP-activated protein kinase undergoes nucleotide-dependent conformational changes Authors: Chen, L. / Wang, J. / Zhang, Y.-Y. / Yan, S.F. / Neumann, D. / Schlattner, U. / Wang, Z.-X. / Wu, J.-W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eak.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eak.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 4eak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4eak_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4eak_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4eak_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 4eak_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/4eak ftp://data.pdbj.org/pub/pdb/validation_reports/ea/4eak | HTTPS FTP |
-Related structure data
Related structure data | 4eagC 4eaiC 4eajC 4ealC 2v8qS C: citing same article (ref.) S: Starting model for refinement |
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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: 12097.888 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Chimera protein of residues 405-479 and residues 540-559 from 5'-AMP-activated protein kinase catalytic subunit alpha-1 (Uniprot P54645), linked by linker GGGGGG Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkaa1, Ampk1 / Production host: Escherichia coli (E. coli) References: UniProt: P54645, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase |
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-5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BC
#2: Protein | Mass: 8133.786 Da / Num. of mol.: 1 / Fragment: UNP residues 200-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkab1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80386 |
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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) / Gene: Prkag1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80385 |
-Non-polymers , 3 types, 77 molecules
#4: Chemical | #5: Chemical | ChemComp-TAM / | #6: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1M MES pH 5.9, 18% IPP, VAPOR DIFFUSION, HANGING DROP, temperature 298 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 18796 / Num. obs: 18796 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 57.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.11 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V8Q Resolution: 2.5→28.631 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.39 / σ(F): 0.13 / Phase error: 26.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.49 Å2 / ksol: 0.342 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.36 Å2 / Biso mean: 72.9033 Å2 / Biso min: 25.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→28.631 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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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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