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Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody

Electron Microscopy
3.47Å resolution
PDB entry 7jhg coloured by chain, front view.
PDB entry 7jhg coloured by chain, side view.
PDB entry 7jhg coloured by chain, top view.
Source organisms:
Assembly composition:
hetero heptamer (preferred)
Entry contents: 7 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: AMPK complex, alpha1-beta2-gamma1 variant and Maltose/maltodextrin-binding periplasmic protein
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Multimeric state: hetero heptamer
Accessible surface area: 75763.86 Å2
Buried surface area: 22614.87 Å2
Dissociation area: 1,582.49 Å2
Dissociation energy (ΔGdiss): -12.65 kcal/mol
Dissociation entropy (TΔSdiss): 27.12 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-238630

Macromolecules

5'-AMP-activated protein kinase catalytic subunit alpha-1
Chain: A
Length: 484 amino acids
Theoretical weight: 56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q13131 (Residues: 22-559; Coverage: 87%)
Gene names: AMPK1, PRKAA1
Pfam:
InterPro:
5'-AMP-activated protein kinase catalytic subunit alpha-1 in PDB entry 7jhg, assembly 1, front view.
5'-AMP-activated protein kinase catalytic subunit alpha-1 in PDB entry 7jhg, assembly 1, side view.
5'-AMP-activated protein kinase catalytic subunit alpha-1 in PDB entry 7jhg, assembly 1, top view.
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5'-AMP-activated protein kinase subunit beta-2
Chain: B
Length: 198 amino acids
Theoretical weight: 22.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O43741 (Residues: 75-272; Coverage: 73%)
Gene name: PRKAB2
Pfam:
InterPro:
5'-AMP-activated protein kinase subunit beta-2 in PDB entry 7jhg, assembly 1, front view.
5'-AMP-activated protein kinase subunit beta-2 in PDB entry 7jhg, assembly 1, side view.
5'-AMP-activated protein kinase subunit beta-2 in PDB entry 7jhg, assembly 1, top view.
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5'-AMP-activated protein kinase subunit gamma-1
Chain: G
Length: 306 amino acids
Theoretical weight: 34.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P54619 (Residues: 24-327; Coverage: 92%)
Gene name: PRKAG1
Pfam: CBS domain
InterPro: CBS domain
5'-AMP-activated protein kinase subunit gamma-1 in PDB entry 7jhg, assembly 1, front view.
5'-AMP-activated protein kinase subunit gamma-1 in PDB entry 7jhg, assembly 1, side view.
5'-AMP-activated protein kinase subunit gamma-1 in PDB entry 7jhg, assembly 1, top view.
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Maltose/maltodextrin-binding periplasmic protein
Chain: M
Length: 373 amino acids
Theoretical weight: 40.83 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0AEX9 (Residues: 25-392; Coverage: 99%)
Gene names: JW3994, b4034, malE
Pfam: Bacterial extracellular solute-binding protein
InterPro:
Maltose/maltodextrin-binding periplasmic protein in PDB entry 7jhg, assembly 1, front view.
Maltose/maltodextrin-binding periplasmic protein in PDB entry 7jhg, assembly 1, side view.
Maltose/maltodextrin-binding periplasmic protein in PDB entry 7jhg, assembly 1, top view.
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Fab light chain
Chain: L
Length: 215 amino acids
Theoretical weight: 23.21 KDa
Source organism: synthetic construct
Expression system: Escherichia coli K-12
InterPro:
Fab light chain in PDB entry 7jhg, assembly 1, front view.
Fab light chain in PDB entry 7jhg, assembly 1, side view.
Fab light chain in PDB entry 7jhg, assembly 1, top view.
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Fab heavy chain
Chain: H
Length: 237 amino acids
Theoretical weight: 25.48 KDa
Source organism: synthetic construct
Expression system: Escherichia coli K-12
InterPro:
Fab heavy chain in PDB entry 7jhg, assembly 1, front view.
Fab heavy chain in PDB entry 7jhg, assembly 1, side view.
Fab heavy chain in PDB entry 7jhg, assembly 1, top view.
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Nanobody
Chain: N
Length: 159 amino acids
Theoretical weight: 17.41 KDa
Source organism: synthetic construct
Expression system: Escherichia coli K-12
InterPro:
Nanobody in PDB entry 7jhg, assembly 1, front view.
Nanobody in PDB entry 7jhg, assembly 1, side view.
Nanobody in PDB entry 7jhg, assembly 1, top view.
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