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Yorodumi- PDB-7jhg: Cryo-EM structure of ATP-bound fully inactive AMPK in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 7jhg | |||||||||
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Title | Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody | |||||||||
Components |
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Keywords | TRANSFERASE/IMMUNE SYSTEM / AMPK / ATP / fully inactive / KD-displaced / TRANSFERASE-IMMUNE SYSTEM complex | |||||||||
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 / positive regulation of peptidyl-lysine acetylation ...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 / bile acid signaling pathway / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / positive regulation of skeletal muscle tissue development / import into nucleus / CAMKK-AMPK signaling cascade / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / nucleotide-activated protein kinase complex / positive regulation of T cell mediated immune response to tumor cell / : / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / negative regulation of hepatocyte apoptotic process / tau-protein kinase / protein kinase regulator activity / cellular response to ethanol / negative regulation of TOR signaling / protein localization to lipid droplet / bile acid and bile salt transport / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / regulation of glycolytic process / motor behavior / positive regulation of protein targeting to mitochondrion / cAMP-dependent protein kinase activity / lipid biosynthetic process / AMP-activated protein kinase activity / tau-protein kinase activity / negative regulation of tubulin deacetylation / Macroautophagy / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / positive regulation of protein kinase activity / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / cellular response to glucose starvation / regulation of microtubule cytoskeleton organization / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of autophagy / Activation of AMPK downstream of NMDARs / response to UV / positive regulation of protein localization / 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 gamma radiation / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / ADP binding / regulation of circadian rhythm / tau protein binding / Wnt signaling pathway / autophagy / fatty acid biosynthetic process / cellular response to hydrogen peroxide / response to estrogen / neuron cellular homeostasis / glucose metabolic process / cellular response to prostaglandin E stimulus / positive regulation of T cell activation / rhythmic process / positive regulation of cold-induced thermogenesis / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / outer membrane-bounded periplasmic space / 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 / protein phosphorylation / apical plasma membrane / axon Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Escherichia coli K-12 (bacteria) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
Authors | Yan, Y. / Murkherjee, S. / Zhou, X.E. / Xu, T.H. / Xu, H.E. / Kossiakoff, A.A. / Melcher, K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2021 Title: Structure of an AMPK complex in an inactive, ATP-bound state. Authors: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna ...Authors: Yan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna Radziwon / Abigail Ellis / Scott J Novick / Irving E Vega / Russell G Jones / Laurence J Miller / H Eric Xu / Patrick R Griffin / Anthony A Kossiakoff / Karsten Melcher / Abstract: Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in ...Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in which the kinase activation loop (AL) is protected from protein phosphatases, thus keeping the AL in its active, phosphorylated state. At low AMP:ATP (adenosine triphosphate) ratios, ATP inhibits AMPK by increasing AL dynamics and accessibility. We developed conformation-specific antibodies to trap ATP-bound AMPK in a fully inactive, dynamic state and determined its structure at 3.5-angstrom resolution using cryo-electron microscopy. A 180° rotation and 100-angstrom displacement of the kinase domain fully exposes the AL. On the basis of the structure and supporting biophysical data, we propose a multistep mechanism explaining how adenine nucleotides and pharmacological agonists modulate AMPK activity by altering AL phosphorylation and accessibility. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jhg.cif.gz | 313.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jhg.ent.gz | 252.8 KB | Display | PDB format |
PDBx/mmJSON format | 7jhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jhg_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7jhg_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7jhg_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 7jhg_validation.cif.gz | 81.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/7jhg ftp://data.pdbj.org/pub/pdb/validation_reports/jh/7jhg | HTTPS FTP |
-Related structure data
Related structure data | 22336MC 7jhhC 7jijC 7m74C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AM
#1: Protein | Mass: 56004.395 Da / Num. of mol.: 1 / Fragment: UNP residues 22-480,535-559 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA1, AMPK1 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q13131, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase |
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#4: Protein | Mass: 40827.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: malE / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C3SHQ8 |
-5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BG
#2: Protein | Mass: 22384.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: O43741 |
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#3: Protein | Mass: 34833.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P54619 |
-Antibody , 3 types, 3 molecules LHN
#5: Antibody | Mass: 23212.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) |
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#6: Antibody | Mass: 25483.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) |
#7: Antibody | Mass: 17414.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) |
-Sugars , 1 types, 1 molecules
#8: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose |
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-Non-polymers , 4 types, 4 molecules
#9: Chemical | ChemComp-TAK / |
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#10: Chemical | ChemComp-ATP / |
#11: Chemical | ChemComp-ADP / |
#12: Chemical | ChemComp-AMP / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.22 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 83 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6157 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Particle selection | Num. of particles selected: 943787 | ||||||||||||||||
3D reconstruction | Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286895 / Symmetry type: POINT | ||||||||||||||||
Atomic model building |
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