› 5gvr

X-ray diffraction
1.5Å resolution

Crystal structure of the DDX41 DEAD domain in an apo closed form

Released:
DOI: 10.2210/pdb5gvr/pdb
PDB entry 5gvr coloured by chain, front view.
PDB entry 5gvr coloured by chain, side view.
PDB entry 5gvr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide.
Omura H, Oikawa D, Nakane T, Kato M, Ishii R, Ishitani R, Tokunaga F, Nureki O
Sci Rep 6 34756 (2016)
PMID: 27721487

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193820 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable ATP-dependent RNA helicase DDX41 Chain: A
Molecule details ›
Chain: A
Length: 234 amino acids
Theoretical weight: 26.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UJV9 (Residues: 169-402; Coverage: 38%)
Gene names: ABS, DDX41
Sequence domains: DEAD/DEAH box helicase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P3221
Unit cell:
a: 81.83Å b: 81.83Å c: 69.57Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.181 0.208
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Inflammatory microenvironment remodelling by tumour cells after radiotherapy.
McLaughlin et al. (2020)
10 more

3 mentions without citation

Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms.
He et al. (2020)
2 more