› 5v4k

X-ray diffraction
2.1Å resolution

Crystal structure of NEDD4 LIR-fused human LC3B_2-119

Released:
DOI: 10.2210/pdb5v4k/pdb
PDB entry 5v4k coloured by chain, front view.
PDB entry 5v4k coloured by chain, side view.
PDB entry 5v4k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into links between autophagy and the ubiquitin system from the structure of LC3B bound to the LIR motif from the E3 ligase NEDD4.
Qiu Y, Zheng Y, Wu KP, Schulman BA
Protein Sci 26 1674-1680 (2017)
PMID: 28470758

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190446 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Microtubule-associated proteins 1A/1B light chain 3B Chains: A, B
Molecule details ›
Chains: A, B
Length: 132 amino acids
Theoretical weight: 15.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9GZQ8 (Residues: 2-119; Coverage: 94%)
Gene names: MAP1ALC3, MAP1LC3B
Sequence domains: Autophagy protein Atg8 ubiquitin like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

2 bound ligands:
Ligand GOL 2 x GOL
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P43212
Unit cell:
a: 69.57Å b: 69.57Å c: 119.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.233
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Regulation of the Tumor-Suppressor BECLIN 1 by Distinct Ubiquitination Cascades.
Boutouja et al. (2017)
3 more

2 mentions without citation

Insights into links between autophagy and the ubiquitin system from the structure of LC3B bound to the LIR motif from the E3 ligase NEDD4.
Qiu et al. (2017)
1 more