7JHH

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of an AMPK complex in an inactive, ATP-bound state.

Yan, Y.Mukherjee, S.Harikumar, K.G.Strutzenberg, T.S.Zhou, X.E.Suino-Powell, K.Xu, T.H.Sheldon, R.D.Lamp, J.Brunzelle, J.S.Radziwon, K.Ellis, A.Novick, S.J.Vega, I.E.Jones, R.G.Miller, L.J.Xu, H.E.Griffin, P.R.Kossiakoff, A.A.Melcher, K.

(2021) Science 373: 413-419

  • DOI: 10.1126/science.abe7565
  • Primary Citation of Related Structures:  
    7JHG, 7JHH, 7JIJ, 7M74

  • PubMed 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 which the kinase activation loop (AL) is protected from protein phosphatases, thus keeping the AL in its active, phosphorylated state ...

    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.


    Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA. karsten.melcher@vai.org.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-1A484Homo sapiensMutation(s): 0 
Gene Names: PRKAA1AMPK1
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
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PHAROS:  Q13131
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UniProt GroupQ13131
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit beta-2B198Homo sapiensMutation(s): 0 
Gene Names: PRKAB2
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Find proteins for O43741 (Homo sapiens)
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PHAROS:  O43741
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit gamma-1C [auth G]306Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
UniProt & NIH Common Fund Data Resources
Find proteins for P54619 (Homo sapiens)
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PHAROS:  P54619
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UniProt GroupP54619
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Maltodextrin-binding proteinD [auth M]373Escherichia coli K-12Mutation(s): 0 
Gene Names: malEb4034JW3994
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chainE [auth L]215synthetic constructMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Fab heavy chainF [auth H]237synthetic constructMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NanobodyG [auth N]159synthetic constructMutation(s): 0 
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Oligosaccharides

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Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseH [auth C]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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I [auth G]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

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J [auth G]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
K [auth G]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 8
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
H [auth C]alpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM117372
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM129436

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references