› 5yik

X-ray diffraction
3.1Å resolution

Structure of a Legionella effector with its substrate

Released:
DOI: 10.2210/pdb5yik/pdb
PDB entry 5yik coloured by chain, front view.
PDB entry 5yik coloured by chain, side view.
PDB entry 5yik coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of ubiquitin modification by the Legionella effector SdeA.
Dong Y, Mu Y, Xie Y, Zhang Y, Han Y, Zhou Y, Wang W, Liu Z, Wu M, Wang H, Pan M, Xu N, Xu CQ, Yang M, Fan S, Deng H, Tan T, Liu X, Liu L, Li J, Wang J, Fang X, Feng Y
Nature 557 674-678 (2018)
PMID: 29795342

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143315 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
SdeA Chain: A
Molecule details ›
Chain: A
Length: 968 amino acids
Theoretical weight: 109.79 KDa
Source organism: Legionella pneumophila
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6RCR0 (Residues: 236-1195; Coverage: 64%)
Sequence domains:
Ubiquitin Chains: C, D, F
Molecule details ›
Chains: C, D, F
Length: 78 amino acids
Theoretical weight: 8.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2
Unit cell:
a: 108.846Å b: 145.893Å c: 104.088Å
α: 90° β: 104.46° γ: 90°
R-values:
R R work R free
0.226 0.223 0.279
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Post-translational regulation of ubiquitin signaling.
Song et al. (2019)
11 more

3 mentions without citation

Uncovering the Structural Basis of a New Twist in Protein Ubiquitination.
Puvar et al. (2019)
2 more