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Yorodumi- EMDB-22336: Cryo-EM structure of ATP-bound fully inactive AMPK in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22336 | |||||||||
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Title | Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody | |||||||||
Map data | Structure of AMPK in complex with CpdC and Fab-nanobody | |||||||||
Sample |
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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 / nucleotide-activated protein kinase complex / : / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / 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 / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / regulation of glycolytic process / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / cAMP-dependent protein kinase activity / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / Macroautophagy / tau-protein kinase activity / positive regulation of protein localization / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / cellular response to nutrient levels / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / 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 / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / response to gamma radiation / cellular response to glucose stimulus / TP53 Regulates Metabolic Genes / tau protein binding / 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 / outer membrane-bounded periplasmic space / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
Authors | Yan Y / Murkherjee S / Zhou XE / Xu TH / Xu HE / Kossiakoff AA / Melcher K | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22336.map.gz | 3.9 MB | EMDB map data format | |
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Header (meta data) | emd-22336-v30.xml emd-22336.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22336_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_22336.png | 182.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22336 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22336 | HTTPS FTP |
-Validation report
Summary document | emd_22336_validation.pdf.gz | 354.6 KB | Display | EMDB validaton report |
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Full document | emd_22336_full_validation.pdf.gz | 354.1 KB | Display | |
Data in XML | emd_22336_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_22336_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22336 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22336 | HTTPS FTP |
-Related structure data
Related structure data | 7jhgMC 7jhhC 7jijC 7m74C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22336.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of AMPK in complex with CpdC and Fab-nanobody | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.029 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Cryo-EM structure of ATP-bound fully inactive AMPK in complex wit...
+Supramolecule #1: Cryo-EM structure of ATP-bound fully inactive AMPK in complex wit...
+Supramolecule #2: ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compo...
+Supramolecule #3: Fab-nanobody
+Macromolecule #1: 5'-AMP-activated protein kinase catalytic subunit alpha-1
+Macromolecule #2: 5'-AMP-activated protein kinase subunit beta-2
+Macromolecule #3: 5'-AMP-activated protein kinase subunit gamma-1
+Macromolecule #4: Maltodextrin-binding protein
+Macromolecule #5: Fab light chain
+Macromolecule #6: Fab heavy chain
+Macromolecule #7: Nanobody
+Macromolecule #9: 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a...
+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #12: ADENOSINE MONOPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 6157 / Average exposure time: 0.2 sec. / Average electron dose: 83.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |