4naw

X-ray diffraction
2.2Å resolution

Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3

Released:
Source organism: Homo sapiens
Primary publication:
Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12.
Proc Natl Acad Sci U S A 110 18844-9 (2013)
PMID: 24191030

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131766 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin-like protein ATG12 Chains: A, E, I, M
Molecule details ›
Chains: A, E, I, M
Length: 91 amino acids
Theoretical weight: 10.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O94817 (Residues: 52-140; Coverage: 64%)
Gene names: APG12, APG12L, ATG12
Sequence domains: Ubiquitin-like autophagy protein Apg12
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Autophagy protein 5 Chains: B, F, J, N
Molecule details ›
Chains: B, F, J, N
Length: 275 amino acids
Theoretical weight: 32.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H1Y0 (Residues: 1-275; Coverage: 100%)
Gene names: APG5L, ASP, ATG5
Sequence domains:
Structure domains:
Autophagy-related protein 16-1 Chains: C, G, K, O
Molecule details ›
Chains: C, G, K, O
Length: 36 amino acids
Theoretical weight: 4.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q676U5 (Residues: 11-43; Coverage: 5%)
Gene names: APG16L, ATG16L1, UNQ9393/PRO34307
Ubiquitin-like-conjugating enzyme ATG3 Chains: D, H, L, P
Molecule details ›
Chains: D, H, L, P
Length: 34 amino acids
Theoretical weight: 3.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NT62 (Residues: 140-170; Coverage: 10%)
Gene names: APG3, APG3L, ATG3

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P212121
Unit cell:
a: 93.584Å b: 120.097Å c: 189.466Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.172 0.215
Expression system: Escherichia coli BL21(DE3)