› 7f69

X-ray diffraction
1.5Å resolution

Crystal structure of WIPI2b in complex with ATG16L1

Released:
DOI: 10.2210/pdb7f69/pdb
PDB entry 7f69 coloured by chain, front view.
PDB entry 7f69 coloured by chain, side view.
PDB entry 7f69 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
ATG16L1 adopts a dual-binding site mode to interact with WIPI2b in autophagy.
Gong X, Wang Y, Tang Y, Wang Y, Zhang M, Li M, Zhang Y, Pan L
OpenAccess logo Sci Adv 9 eadf0824 (2023)
PMID: 36857448

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179297 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
WD repeat domain phosphoinositide-interacting protein 2 Chain: A
Molecule details ›
Chain: A
Length: 354 amino acids
Theoretical weight: 39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y4P8 (Residues: 13-379; Coverage: 77%)
  • Best match: Q9Y4P8-2 (Residues: 13-361)
Gene names: CGI-50, WIPI2
Sequence domains: PROPPIN
Autophagy-related protein 16-1 Chain: C
Molecule details ›
Chain: C
Length: 34 amino acids
Theoretical weight: 3.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q676U5 (Residues: 207-236; Coverage: 5%)
Gene names: APG16L, ATG16L1, UNQ9393/PRO34307

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P63
Unit cell:
a: 97.944Å b: 97.944Å c: 65.581Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.182 0.197
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Coiled-coil-mediated dimerization of Atg16 is required for binding to the PROPPIN Atg21.
Bueno-Arribas et al. (2023)
1 more