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- EMDB-22337: Cryo-EM structure of ATP-bound fully inactive AMPK in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-22337
TitleCryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody
Map dataStructure of AMPK with Fab and nanobody
Sample
  • Complex: AMPK complex with Fab and nanobody
    • Complex: AMPK
      • Protein or peptide: 5'-AMP-activated protein kinase catalytic subunit alpha-1
      • Protein or peptide: 5'-AMP-activated protein kinase subunit beta-2
      • Protein or peptide: 5'-AMP-activated protein kinase subunit gamma-1
      • Protein or peptide: Maltodextrin-binding protein
    • Complex: Fab, nanobodyFragment antigen-binding
      • Protein or peptide: Fab light chainFragment antigen-binding
      • Protein or peptide: Fab heavy chainFragment antigen-binding
      • Protein or peptide: NanobodySingle-domain antibody
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE MONOPHOSPHATE
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 / cellular response to organonitrogen compound / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / Carnitine metabolism / negative regulation of hepatocyte apoptotic process / 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 / regulation of glycolytic process / lipid biosynthetic process / cAMP-dependent protein kinase activity / 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 / carbohydrate transmembrane transporter activity / positive regulation of protein kinase activity / cellular response to glucose starvation / fatty acid homeostasis / positive regulation of autophagy / negative regulation of lipid catabolic process / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / energy homeostasis / response to UV / 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 / tau protein binding / 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 / outer membrane-bounded periplasmic space / positive regulation of cold-induced thermogenesis / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / apical plasma membrane / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body
Similarity search - Function
PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / KA1 domain/Ssp2, C-terminal / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin E-set / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Maltodextrin-binding protein / 5'-AMP-activated protein kinase subunit beta-2 / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsYan Y / Murkherjee S / Zhou XE / Xu TH / Xu HE / Kossiakoff AA / Melcher K
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM117372 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM129436 United States
CitationJournal: 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
DepositionJul 20, 2020-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateDec 15, 2021-
Current statusDec 15, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
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  • Surface view colored by radius
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-7jhh
  • Surface level: 0.015
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22337.png

Downloads & links

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Map

FileDownload / File: emd_22337.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of AMPK with Fab and nanobody
Voxel sizeX=Y=Z: 1.029 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.04410703 - 0.081703946
Average (Standard dev.)0.00027798326 (±0.0022904756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 246.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z246.960246.960246.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0440.0820.000

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Supplemental data

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Sample components

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Entire : AMPK complex with Fab and nanobody

EntireName: AMPK complex with Fab and nanobody
Components
  • Complex: AMPK complex with Fab and nanobody
    • Complex: AMPK
      • Protein or peptide: 5'-AMP-activated protein kinase catalytic subunit alpha-1
      • Protein or peptide: 5'-AMP-activated protein kinase subunit beta-2
      • Protein or peptide: 5'-AMP-activated protein kinase subunit gamma-1
      • Protein or peptide: Maltodextrin-binding protein
    • Complex: Fab, nanobodyFragment antigen-binding
      • Protein or peptide: Fab light chainFragment antigen-binding
      • Protein or peptide: Fab heavy chainFragment antigen-binding
      • Protein or peptide: NanobodySingle-domain antibody
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: AMPK complex with Fab and nanobody

SupramoleculeName: AMPK complex with Fab and nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Molecular weightTheoretical: 220 KDa

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Supramolecule #2: AMPK

SupramoleculeName: AMPK / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

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Supramolecule #3: Fab, nanobody

SupramoleculeName: Fab, nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#7
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: 5'-AMP-activated protein kinase catalytic subunit alpha-1

MacromoleculeName: 5'-AMP-activated protein kinase catalytic subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.004395 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: VKIGHYILGD TLGVGTFGKV KVGKHELTGH KVAVKILNRQ KIRSLDVVGK IRREIQNLKL FRHPHIIKLY QVISTPSDIF MVMEYVSGG ELFDYICKNG RLDEKESRRL FQQILSGVDY CHRHMVVHRD LKPENVLLDA HMNAKIADFG LSNMMSDGEF L RTSCGSPN ...String:
VKIGHYILGD TLGVGTFGKV KVGKHELTGH KVAVKILNRQ KIRSLDVVGK IRREIQNLKL FRHPHIIKLY QVISTPSDIF MVMEYVSGG ELFDYICKNG RLDEKESRRL FQQILSGVDY CHRHMVVHRD LKPENVLLDA HMNAKIADFG LSNMMSDGEF L RTSCGSPN YAAPEVISGR LYAGPEVDIW SSGVILYALL CGTLPFDDDH VPTLFKKICD GIFYTPQYLN PSVISLLKHM LQ VDPMKRA TIKDIREHEW FKQDLPKYLF PEDPSYSSTM IDDEALKEVC EKFECSEEEV LSCLYNRNHQ DPLAVAYHLI IDN RRIMNE AKDFYLATSP PDSFLDDHHL TRPHPERVPF LVAETPRARH TLDELNPQKS KHQGVRKAKW HLGIRSQSRP NDIM AEVCR AIKQLDYEWK VVNPYYLRVR RKNPVTSTYS KMSLQLYQVD SRTYLLDFRS IDDELTPRPG SHTIEFFEMC ANLIK ILAQ

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Macromolecule #2: 5'-AMP-activated protein kinase subunit beta-2

MacromoleculeName: 5'-AMP-activated protein kinase subunit beta-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.38465 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MARPTVIRWS EGGKEVFISG SFNNWSTKIP LIKSHNDFVA ILDLPEGEHQ YKFFVDGQWV HDPSEPVVTS QLGTINNLIH VKKSDFEVF DALKLDSMES SETSCRDLSS SPPGPYGQEM YAFRSAARFK SPPILPPHLL QVILNKDTNI SCDPALLPEP N HVMLNHLY ...String:
MARPTVIRWS EGGKEVFISG SFNNWSTKIP LIKSHNDFVA ILDLPEGEHQ YKFFVDGQWV HDPSEPVVTS QLGTINNLIH VKKSDFEVF DALKLDSMES SETSCRDLSS SPPGPYGQEM YAFRSAARFK SPPILPPHLL QVILNKDTNI SCDPALLPEP N HVMLNHLY ALSIKDSVMV LSATHRYKKK YVTTLLYKPI

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Macromolecule #3: 5'-AMP-activated protein kinase subunit gamma-1

MacromoleculeName: 5'-AMP-activated protein kinase subunit gamma-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.833359 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MGSNNSVYTS FMKSHRCYDL IPTSSKLVVF DTSLQVKKAF FALVTNGVRA APLWDSKKQS FVGMLTITDF INILHRYYKS ALVQIYELE EHKIETWREV YLQDSFKPLV CISPNASLFD AVSSLIRNKI HRLPVIDPES GNTLYILTHK RILKFLKLFI T EFPKPEFM ...String:
MGSNNSVYTS FMKSHRCYDL IPTSSKLVVF DTSLQVKKAF FALVTNGVRA APLWDSKKQS FVGMLTITDF INILHRYYKS ALVQIYELE EHKIETWREV YLQDSFKPLV CISPNASLFD AVSSLIRNKI HRLPVIDPES GNTLYILTHK RILKFLKLFI T EFPKPEFM SKSLEELQIG TYANIAMVRT TTPVYVALGI FVQHRVSALP VVDEKGRVVD IYSKFDVINL AAEKTYNNLD VS VTKALQH RSHYFEGVLK CYLHETLETI INRLVEAEVH RLVVVDENDV VKGIVSLSDI LQALVLTGG

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Macromolecule #4: Maltodextrin-binding protein

MacromoleculeName: Maltodextrin-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 40.827125 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPAAAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL MFNLQEPYFT W PLIAADGG ...String:
MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPAAAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL MFNLQEPYFT W PLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NGPWAWSNID TS AVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYEEELAKDP RIA ATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTNAAEF

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Macromolecule #5: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.212715 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSGPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSGPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #6: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.483488 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NIYYYSIHWV RQAPGKGLEW VASIYPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYYPYFISY YSKMEAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NIYYYSIHWV RQAPGKGLEW VASIYPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYYPYFISY YSKMEAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCDKTHT

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Macromolecule #7: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.414383 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMHHHHHHG ENLYFQGSQV QLQESGGGLV QPGGSLRLSC AASGRTISRY AMSWFRQAPG KEREFVAVA RRSGDGAFYA DSVQGRFTVS RDDAKNTVYL QMNSLKPEDT AVYYCAIDSD TFYSGSYDYW GQGTQVTVSS

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #11: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 7659 / Average exposure time: 0.2 sec. / Average electron dose: 88.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1501939
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 360824
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

4rer

,

6cmo

,

6h16

)
Output model

PDB-7jhh:
Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody

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