+Open data
-Basic information
Entry | Database: PDB / ID: 4cfh | |||||||||
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Title | Structure of an active form of mammalian AMPK | |||||||||
Components |
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Keywords | TRANSFERASE / TRANSFERASE PHOSPHORYLATION / ACTIVE FORM / NUCLEOTIDE-BINDING / STAUROSPORINE-BINDING / SERINE/THREONINE-PROTEIN KINASE | |||||||||
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 / 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 / negative regulation of lipid catabolic process / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 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. #1: Journal: Nat.Commun. / Year: 2013 Title: Structural Basis of Ampk Regulation by Small Molecule Activators. Authors: Xiao, B. / Sanders, M.J. / Carmena, D. / Bright, N.J. / Haire, L.F. / Underwood, E. / Patel, B.R. / Heath, R.B. / Walker, P.A. / Hallen, S. / Giordanetto, F. / 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 | 4cfh.cif.gz | 348.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cfh.ent.gz | 280.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cfh ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cfh | HTTPS FTP |
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-Related structure data
Related structure data | 2y8lC 2y8qC 2ya3C 2h6dS 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
-5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA- ... , 2 types, 2 molecules AC
#1: Protein | Mass: 57248.484 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-481 Source method: isolated from a genetically manipulated source Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE ALPHA SUBUNIT AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 TO 524), RESIDUES 471 TO 523 WERE REMOVED FROM ...Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE ALPHA SUBUNIT AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 TO 524), RESIDUES 471 TO 523 WERE REMOVED FROM THE PROTEIN, RESIDUES 523 TO 548 ARE GIVEN AS CHAIN C 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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#3: Protein/peptide | Mass: 3064.600 Da / Num. of mol.: 1 / Fragment: RESIDUES 535-559 Source method: isolated from a genetically manipulated source Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE SUBUNIT ALPHA AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 AND 524), RESIDUES 471 TO 523 WERE REMOVED FROM ...Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE SUBUNIT ALPHA AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 AND 524), RESIDUES 471 TO 523 WERE REMOVED FROM THE PROTEIN, RESIDUES 2 TO 470 ARE GIVEN AS CHAIN A Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P54645, non-specific serine/threonine protein kinase |
-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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#4: 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 , 2 types, 3 molecules
#5: Chemical | ChemComp-STU / |
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#6: Chemical |
-Details
Sequence details | U40819 IN PUBMED. THE 19 RESIDUES (MSHHHHHHSSGLEVLFQGP)AT THE N-TERMINAL ARE EXPRESSION TAG. ...U40819 IN PUBMED. THE 19 RESIDUES (MSHHHHHHSS |
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-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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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 8% ISOPROPANOL AND 5% MPD AS PRECIPITANT IN 0.1M TRIS AT PH 7.5 AT 18 DEGREES. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9791 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.24→29.53 Å / Num. obs: 18662 / % possible obs: 93.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.24→3.44 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2V8Q AND 2H6D Resolution: 3.24→29.53 Å / σ(F): 1.33 / Stereochemistry target values: ML
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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: 3.24→29.53 Å
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LS refinement shell |
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