› 5dpt

X-ray diffraction
2.9Å resolution

Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117

Released:
DOI: 10.2210/pdb5dpt/pdb
PDB entry 5dpt coloured by chain, front view.
PDB entry 5dpt coloured by chain, side view.
PDB entry 5dpt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and functional analysis of the GABARAP interaction motif (GIM).
Rogov VV, Stolz A, Ravichandran AC, Rios-Szwed DO, Suzuki H, Kniss A, Löhr F, Wakatsuki S, Dötsch V, Dikic I, Dobson RC, McEwan DG
EMBO Rep 18 1382-1396 (2017)
PMID: 28655748

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190489 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Gamma-aminobutyric acid receptor-associated protein-like 1; Pleckstrin homology domain-containing family M member 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 132 amino acids
Theoretical weight: 15.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y4G2 (Residues: 627-638; Coverage: 1%)
  • Canonical: Q9H0R8 (Residues: 2-117; Coverage: 99%)
Gene names: GABARAPL1, GEC1, KIAA0356, PLEKHM1
Sequence domains: Autophagy protein Atg8 ubiquitin like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

1 bound ligand:
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P3221
Unit cell:
a: 84.791Å b: 84.791Å c: 105.44Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.216 0.214 0.26
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

32 review citations

Autophagy and autophagy-related proteins in cancer.
Li et al. (2020)
31 more

5 mentions without citation

Structural and functional analysis of the GABARAP interaction motif (GIM).
Rogov et al. (2017)
4 more