› 6hoh

X-ray diffraction
2.25Å resolution

Structure of VPS34 LIR motif (S249E) bound to GABARAP

Released:
DOI: 10.2210/pdb6hoh/pdb
PDB entry 6hoh coloured by chain, front view.
PDB entry 6hoh coloured by chain, side view.
PDB entry 6hoh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.
Birgisdottir ÅB, Mouilleron S, Bhujabal Z, Wirth M, Sjøttem E, Evjen G, Zhang W, Lee R, O'Reilly N, Tooze SA, Lamark T, Johansen T
Autophagy 15 1333-1355 (2019)
PMID: 30767700

Function and Biology Details

Reaction catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol = ADP + 1-phosphatidyl-1D-myo-inositol 3-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131839 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Gamma-aminobutyric acid receptor-associated protein; Phosphatidylinositol 3-kinase catalytic subunit type 3 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 129 amino acids
Theoretical weight: 15.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NEB9 (Residues: 244-258; Coverage: 2%)
  • Canonical: O95166 (Residues: 1-112; Coverage: 96%)
Gene names: FLC3B, GABARAP, HT004, PIK3C3, VPS34
Sequence domains: Autophagy protein Atg8 ubiquitin like

Ligands and Environments

1 bound ligand:
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P213
Unit cell:
a: 119.502Å b: 119.502Å c: 119.502Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.25
Expression system: Escherichia coli

Quick links

Citations

22 review citations

Emerging roles of ATG proteins and membrane lipids in autophagosome formation.
Nishimura et al. (2020)
21 more

1 mention without citation

Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study.
Ware et al. (2021)