› 5f0m

X-ray diffraction
3.1Å resolution

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)

Released:
DOI: 10.2210/pdb5f0m/pdb
PDB entry 5f0m coloured by chain, front view.
PDB entry 5f0m coloured by chain, side view.
PDB entry 5f0m 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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-129992 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 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: 321 amino acids
Theoretical weight: 37.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75436 (Residues: 1-321; Coverage: 98%)
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
Natural resistance-associated macrophage protein 2 Chain: D
Molecule details ›
Chain: D
Length: 18 amino acids
Theoretical weight: 2.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49281 (Residues: 549-560; Coverage: 2%)
Gene names: DCT1, DMT1, NRAMP2, OK/SW-cl.20, SLC11A2

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand GOL 5 x GOL
Ligand EDO 12 x EDO
1 modified residue:
Ligand MSE 9 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 369.48Å b: 74.91Å c: 57.39Å
α: 90° β: 97.64° γ: 90°
R-values:
R R work R free
0.212 0.21 0.254
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

35 review citations

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

2 mentions without citation

Structural Mechanism for Cargo Recognition by the Retromer Complex.
Lucas et al. (2016)
1 more