› 5cra

X-ray diffraction
2.64Å resolution

Structure of the SdeA DUB Domain

Released:
DOI: 10.2210/pdb5cra/pdb
PDB entry 5cra coloured by chain, front view.
PDB entry 5cra coloured by chain, side view.
PDB entry 5cra coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination.
Sheedlo MJ, Qiu J, Tan Y, Paul LN, Luo ZQ, Das C
Proc Natl Acad Sci U S A 112 15090-5 (2015)
PMID: 26598703

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143278 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
SdeA Chains: A, B
Molecule details ›
Chains: A, B
Length: 193 amino acids
Theoretical weight: 20.98 KDa
Source organism: Legionella pneumophila
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q6RCR0 (Residues: 6-198; Coverage: 13%)
Sequence domains: SidE DUB domain
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 75 amino acids
Theoretical weight: 8.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-227; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand SO4 9 x SO4
Ligand GVE 2 x GVE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P32
Unit cell:
a: 64.192Å b: 64.192Å c: 120.717Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.184 0.236
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli

Quick links

Citations

26 review citations

Legionella and Coxiella effectors: strength in diversity and activity.
Qiu et al. (2017)
25 more

7 mentions without citation

Synthetic and semi-synthetic strategies to study ubiquitin signaling.
van Tilburg et al. (2016)
6 more