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Yorodumi- PDB-7myj: Structure of full length human AMPK (a2b1g1) in complex with a sm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7myj | ||||||||||||||||||
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Title | Structure of full length human AMPK (a2b1g1) in complex with a small molecule activator MSG011 | ||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Activator / Kinase / AMPK | ||||||||||||||||||
Function / homology | Function and homology information [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy ...[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / import into nucleus / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / negative regulation of hepatocyte apoptotic process / protein kinase regulator activity / protein localization to lipid droplet / negative regulation of TOR signaling / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process / Nuclear events mediated by NFE2L2 / lipid biosynthetic process / cAMP-dependent protein kinase activity / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / Macroautophagy / positive regulation of protein localization / AMP binding / cholesterol biosynthetic process / cellular response to nutrient levels / positive regulation of macroautophagy / positive regulation of protein kinase activity / regulation of macroautophagy / fatty acid homeostasis / cellular response to glucose starvation / positive regulation of autophagy / energy homeostasis / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / negative regulation of TORC1 signaling / cellular response to calcium ion / protein serine/threonine/tyrosine kinase activity / positive regulation of glycolytic process / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / TP53 Regulates Metabolic Genes / regulation of circadian rhythm / ADP binding / Wnt signaling pathway / fatty acid biosynthetic process / autophagy / cytoplasmic stress granule / cellular response to prostaglandin E stimulus / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / 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 gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||||||||||||||
Authors | Ovens, A.J. / Gee, Y.S. / Ling, N.X.Y. / Waters, N.J. / Yu, D. / Scott, J.W. / Parker, M.W. / Hoffman, N.J. / Kemp, B.E. / Baell, J.B. ...Ovens, A.J. / Gee, Y.S. / Ling, N.X.Y. / Waters, N.J. / Yu, D. / Scott, J.W. / Parker, M.W. / Hoffman, N.J. / Kemp, B.E. / Baell, J.B. / Oakhill, J.S. / Langendorf, C.G. | ||||||||||||||||||
Funding support | Australia, 5items
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Citation | Journal: Biochem.J. / Year: 2022 Title: Structure-function analysis of the AMPK activator SC4 and identification of a potent pan AMPK activator. Authors: Ovens, A.J. / Gee, Y.S. / Ling, N.X.Y. / Yu, D. / Hardee, J.P. / Chung, J.D. / Ngoei, K.R.W. / Waters, N.J. / Hoffman, N.J. / Scott, J.W. / Loh, K. / Spengler, K. / Heller, R. / Parker, M.W. ...Authors: Ovens, A.J. / Gee, Y.S. / Ling, N.X.Y. / Yu, D. / Hardee, J.P. / Chung, J.D. / Ngoei, K.R.W. / Waters, N.J. / Hoffman, N.J. / Scott, J.W. / Loh, K. / Spengler, K. / Heller, R. / Parker, M.W. / Lynch, G.S. / Huang, F. / Galic, S. / Kemp, B.E. / Baell, J.B. / Oakhill, J.S. / Langendorf, C.G. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7myj.cif.gz | 769.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7myj.ent.gz | 625.3 KB | Display | PDB format |
PDBx/mmJSON format | 7myj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7myj_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7myj_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7myj_validation.xml.gz | 65.2 KB | Display | |
Data in CIF | 7myj_validation.cif.gz | 86.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/7myj ftp://data.pdbj.org/pub/pdb/validation_reports/my/7myj | HTTPS FTP |
-Related structure data
Related structure data | 6b1uS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 63918.051 Da / Num. of mol.: 2 / Mutation: D271G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA2, AMPK, AMPK2 / Production host: Escherichia coli (E. coli) References: UniProt: P54646, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase |
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-5'-AMP-activated protein kinase subunit ... , 2 types, 4 molecules BDEF
#2: Protein | Mass: 30504.299 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y478 #3: Protein | Mass: 38225.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54619 |
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-Non-polymers , 3 types, 8 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-AMP / |
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-Details
Has ligand of interest | Y |
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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: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 8-10% PEG3350, 1% glucose, 0.1 M magnesium chloride, 0.1 M imidazole, 0.0005-0.003% CAPB |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.71073 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71073 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→48.72 Å / Num. obs: 59194 / % possible obs: 98.91 % / Redundancy: 2.4 % / Biso Wilson estimate: 70.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.053 / Rrim(I) all: 0.075 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.95→3.055 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5846 / CC1/2: 0.735 / Rpim(I) all: 0.369 / Rrim(I) all: 0.523 / % possible all: 97.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6B1U Resolution: 2.95→48.72 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.906 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 9.338 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.277 / SU Rfree Blow DPI: 0.342 / SU Rfree Cruickshank DPI: 0.358
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Displacement parameters | Biso mean: 76.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→48.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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