› 4rer

X-ray diffraction
4.05Å resolution

Crystal structure of the phosphorylated human alpha1 beta2 gamma1 holo-AMPK complex bound to AMP and cyclodextrin

Released:
DOI: 10.2210/pdb4rer/pdb
PDB entry 4rer coloured by chain, front view.
PDB entry 4rer coloured by chain, side view.
PDB entry 4rer coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of AMPK regulation by adenine nucleotides and glycogen.
Li X, Wang L, Zhou XE, Ke J, de Waal PW, Gu X, Tan MH, Wang D, Wu D, Xu HE, Melcher K
Cell Res 25 50-66 (2015)
PMID: 25412657

Function and Biology Details

Reactions catalysed: 
ATP + a protein = ADP + a phosphoprotein
ATP + [tau protein] = ADP + [tau protein] phosphate
ATP + [hydroxymethylglutaryl-CoA reductase (NADPH)] = ADP + [hydroxymethylglutaryl-CoA reductase (NADPH)] phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129097 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
5'-AMP-activated protein kinase catalytic subunit alpha-1 Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 61.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13131 (Residues: 20-559; Coverage: 97%)
Gene names: AMPK1, PRKAA1
Sequence domains:
5'-AMP-activated protein kinase subunit beta-2 Chain: B
Molecule details ›
Chain: B
Length: 197 amino acids
Theoretical weight: 22.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O43741 (Residues: 76-272; Coverage: 72%)
Gene name: PRKAB2
Sequence domains:
5'-AMP-activated protein kinase subunit gamma-1 Chain: G
Molecule details ›
Chain: G
Length: 304 amino acids
Theoretical weight: 34.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P54619 (Residues: 24-327; Coverage: 92%)
Gene name: PRKAG1
Sequence domains: CBS domain

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC
Carbohydrate polymer
3 bound ligands:
Ligand STU 1 x STU
Ligand EPE 1 x EPE
Ligand AMP 3 x AMP
2 modified residues:
Ligand TPO 1 x TPO
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P3221
Unit cell:
a: 132.566Å b: 132.566Å c: 195.392Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.227 0.224 0.26
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

29 review citations

AMPK: Mechanisms of Cellular Energy Sensing and Restoration of Metabolic Balance.
Garcia et al. (2017)
28 more

22 mentions without citation

AMPK: An Energy-Sensing Pathway with Multiple Inputs and Outputs.
Hardie et al. (2016)
21 more