› 5osi

X-ray diffraction
2.52Å resolution

Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)

Released:
DOI: 10.2210/pdb5osi/pdb
PDB entry 5osi coloured by chain, front view.
PDB entry 5osi coloured by chain, side view.
PDB entry 5osi coloured by chain, top view.
Source organisms:
Primary publication:
Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL.
Romano-Moreno M, Rojas AL, Williamson CD, Gershlick DC, Lucas M, Isupov MN, Bonifacino JS, Machner MP, Hierro A
Proc Natl Acad Sci U S A 114 E11151-E11160 (2017)
PMID: 29229824

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero dimer
PDBe Complex ID:
PDB-CPX-178615 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Vacuolar protein sorting-associated protein 29 Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 182 amino acids
Theoretical weight: 20.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBQ0 (Residues: 1-182; Coverage: 100%)
Gene names: DC15, DC7, MDS007, VPS29
Sequence domains: Calcineurin-like phosphoesterase superfamily domain
Structure domains: Purple Acid Phosphatase; chain A, domain 2
Vacuolar protein sorting-associated protein 35 Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 311 amino acids
Theoretical weight: 35.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96QK1 (Residues: 471-781; Coverage: 39%)
Gene names: MEM3, TCCCTA00141, VPS35
Sequence domains: Vacuolar protein sorting-associated protein 35
Structure domains: Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C
Interaptin Chains: C, F, I
Molecule details ›
Chains: C, F, I
Length: 14 amino acids
Theoretical weight: 1.6 KDa
Source organism: Legionella pneumophila subsp. pneumophila ATCC 43290
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5ZT54 (Residues: 163-176; Coverage: 1%)
Gene name: lpg2311

Ligands and Environments

2 bound ligands:
Ligand EDO 11 x EDO
Ligand NA 4 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P21
Unit cell:
a: 58.554Å b: 138.993Å c: 126.637Å
α: 90° β: 92.78° γ: 90°
R-values:
R R work R free
0.208 0.205 0.267
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Endosomal receptor trafficking: Retromer and beyond.
Wang et al. (2018)
8 more

2 mentions without citation

Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL.
Romano-Moreno et al. (2017)
1 more