› 5wyh

X-ray diffraction
2.46Å resolution

Crystal structure of RidL(1-200) complexed with VPS29

Released:
DOI: 10.2210/pdb5wyh/pdb
PDB entry 5wyh coloured by chain, front view.
PDB entry 5wyh coloured by chain, side view.
PDB entry 5wyh coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of inhibition of retromer transport by the bacterial effector RidL.
Yao J, Yang F, Sun X, Wang S, Gan N, Liu Q, Liu D, Zhang X, Niu D, Wei Y, Ma C, Luo ZQ, Sun Q, Jia D
Proc Natl Acad Sci U S A 115 E1446-E1454 (2018)
PMID: 29386389

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166296 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Vacuolar protein sorting-associated protein 29 Chains: A, C
Molecule details ›
Chains: A, C
Length: 185 amino acids
Theoretical weight: 20.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBQ0 (Residues: 2-182; Coverage: 100%)
Gene names: DC15, DC7, MDS007, VPS29
Sequence domains: Calcineurin-like phosphoesterase superfamily domain
Structure domains: Purple Acid Phosphatase; chain A, domain 2
Interaptin Chains: B, D
Molecule details ›
Chains: B, D
Length: 198 amino acids
Theoretical weight: 22.89 KDa
Source organism: Legionella pneumophila subsp. pneumophila ATCC 43290
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AichiSR BEAMLINE BL2S1
Spacegroup: P1
Unit cell:
a: 44.312Å b: 82.049Å c: 87.332Å
α: 101.73° β: 104.26° γ: 104.77°
R-values:
R R work R free
0.191 0.19 0.225
Expression system: Escherichia coli

Quick links

Citations

11 review citations

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

2 mentions without citation

Mechanism of inhibition of retromer transport by the bacterial effector RidL.
Yao et al. (2018)
1 more