› 3ber

X-ray diffraction
1.4Å resolution

Human DEAD-box RNA-helicase DDX47, conserved domain I in complex with AMP

Released:
DOI: 10.2210/pdb3ber/pdb
PDB entry 3ber coloured by chain, front view.
PDB entry 3ber coloured by chain, side view.
PDB entry 3ber coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Comparative structural analysis of human DEAD-box RNA helicases.
Schütz P, Karlberg T, van den Berg S, Collins R, Lehtiö L, Högbom M, Holmberg-Schiavone L, Tempel W, Park HW, Hammarström M, Moche M, Thorsell AG, Schüler H
PLoS One 5 (2010)
PMID: 20941364

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190496 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable ATP-dependent RNA helicase DDX47 Chain: A
Molecule details ›
Chain: A
Length: 249 amino acids
Theoretical weight: 27.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H0S4 (Residues: 5-230; Coverage: 50%)
Gene name: DDX47
Sequence domains: DEAD/DEAH box helicase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

3 bound ligands:
Ligand PO4 1 x PO4
Ligand AMP 1 x AMP
Ligand PGE 2 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 93.05Å b: 70.37Å c: 35.86Å
α: 90° β: 90.7° γ: 90°
R-values:
R R work R free
0.167 0.165 0.189
Expression system: Escherichia coli

Quick links

Citations

16 review citations

Dbp5, Gle1-IP6 and Nup159: a working model for mRNP export.
Folkmann et al. (2011)
15 more

4 mentions without citation

Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins.
Squeglia et al. (2020)
3 more