+Open data
-Basic information
Entry | Database: PDB / ID: 7m74 | ||||||
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Title | ATP-bound AMP-activated protein kinase | ||||||
Components |
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Keywords | SIGNALING PROTEIN / AMPK / activation / ATP-binding | ||||||
Function / homology | Function and homology information AMPK inhibits chREBP transcriptional activation activity / 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 / protein kinase regulator activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process ...AMPK inhibits chREBP transcriptional activation activity / 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 / protein kinase regulator activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process / cAMP-dependent protein kinase activity / Macroautophagy / AMP binding / carbohydrate transmembrane transporter activity / positive regulation of protein kinase activity / cellular response to nutrient levels / Activation of AMPK downstream of NMDARs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / ADP binding / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / periplasmic space / protein kinase activity / protein phosphorylation / positive regulation of gene expression / protein kinase binding / signal transduction / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) Lama glama (llama) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.93 Å | ||||||
Authors | Yan, Y. / Mukherjee, S. / Harikumar, K.G. / Strutzenberg, T. / Zhou, X.E. / Powell, S.K. / Xu, T. / Sheldon, R. / Lamp, J. / Brunzelle, J.S. ...Yan, Y. / Mukherjee, S. / Harikumar, K.G. / Strutzenberg, T. / Zhou, X.E. / Powell, S.K. / Xu, T. / Sheldon, R. / Lamp, J. / Brunzelle, J.S. / Radziwon, K. / Ellis, A. / Novick, S.J. / Vega, I.E. / Jones, R. / Miller, L.J. / Xu, H.E. / Griffin, P.R. / Kossiakoff, A.A. / Melcher, K. | ||||||
Funding support | United States, 1items
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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 | 7m74.cif.gz | 312.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m74.ent.gz | 252.7 KB | Display | PDB format |
PDBx/mmJSON format | 7m74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/7m74 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/7m74 | HTTPS FTP |
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-Related structure data
Related structure data | 23708MC 7jhgC 7jhhC 7jijC M: map data used to model this data 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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-Components
-Protein , 2 types, 2 molecules AM
#1: Protein | Mass: 56004.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA1, AMPK1 / Production host: Spodoptera frugiperda (fall armyworm) References: non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [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 (E. coli) / Gene: malE, GRW33_05015 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6D0N546 |
-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: Spodoptera frugiperda (fall armyworm) / 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54619 |
-Antibody , 3 types, 3 molecules LHN
#5: Antibody | Mass: 22794.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#6: Antibody | Mass: 24466.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#7: Antibody | Mass: 13159.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
-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 | Name: MBP-fused ATP bound AMPK in complex with C-compound stabilized by Fab and a nanobody Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
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: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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 / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-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: 3918314 | |||||||||
3D reconstruction | Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 569379 / Symmetry type: POINT |