› 4afi

X-ray diffraction
2.8Å resolution

Complex between Vamp7 longin domain and fragment of delta-adaptin from AP3

Released:
DOI: 10.2210/pdb4afi/pdb
PDB entry 4afi coloured by chain, front view.
PDB entry 4afi coloured by chain, side view.
PDB entry 4afi coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of the intracellular sorting of the SNARE VAMP7 by the AP3 adaptor complex.
Kent HM, Evans PR, Schäfer IB, Gray SR, Sanderson CM, Luzio JP, Peden AA, Owen DJ
Dev Cell 22 979-88 (2012)
PMID: 22521722

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127020 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
AP-3 complex subunit delta-1; Vesicle-associated membrane protein 7 Chains: A, B
Molecule details ›
Chains: A, B
Length: 173 amino acids
Theoretical weight: 19.56 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O14617 (Residues: 680-729; Coverage: 4%)
  • Canonical: P70280 (Residues: 1-120; Coverage: 55%)
Gene names: AP3D1, PRO0039, Sybl1, Vamp7
Sequence domains:
Structure domains: Longin domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43212
Unit cell:
a: 63.555Å b: 63.555Å c: 217.915Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.231 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

The biogenesis of lysosomes and lysosome-related organelles.
Luzio et al. (2014)
9 more

3 mentions without citation

Cargo recognition in clathrin-mediated endocytosis.
Traub et al. (2013)
2 more