› 5f0j

X-ray diffraction
2.7Å resolution

Structure of retromer VPS26-VPS35 subunits bound to SNX3

Released:
DOI: 10.2210/pdb5f0j/pdb
PDB entry 5f0j coloured by chain, front view.
PDB entry 5f0j coloured by chain, side view.
PDB entry 5f0j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Mechanism for Cargo Recognition by the Retromer Complex.
Lucas M, Gershlick DC, Vidaurrazaga A, Rojas AL, Bonifacino JS, Hierro A
Cell 167 1623-1635.e14 (2016)
PMID: 27889239

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-129993 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Vacuolar protein sorting-associated protein 35 Chain: A
Molecule details ›
Chain: A
Length: 462 amino acids
Theoretical weight: 53.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96QK1 (Residues: 14-470; Coverage: 57%)
Gene names: MEM3, TCCCTA00141, VPS35
Sequence domains: Vacuolar protein sorting-associated protein 35
Vacuolar protein sorting-associated protein 26A Chain: B
Molecule details ›
Chain: B
Length: 341 amino acids
Theoretical weight: 40.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75436 (Residues: 2-326; Coverage: 99%)
Gene names: VPS26, VPS26A
Sequence domains: Vacuolar protein sorting-associated protein 26
Structure domains: Immunoglobulin-like
Sorting nexin-3 Chain: C
Molecule details ›
Chain: C
Length: 167 amino acids
Theoretical weight: 19.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O60493 (Residues: 1-162; Coverage: 100%)
Gene name: SNX3
Sequence domains: PX domain
Structure domains: Phox-like domain

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand GOL 5 x GOL
Ligand EDO 24 x EDO
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: C2
Unit cell:
a: 372.82Å b: 75.58Å c: 57.53Å
α: 90° β: 97.87° γ: 90°
R-values:
R R work R free
0.209 0.207 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

33 review citations

To degrade or not to degrade: mechanisms and significance of endocytic recycling.
Cullen et al. (2018)
32 more

10 mentions without citation

Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development.
Mallam et al. (2017)
9 more