› 5elx

X-ray diffraction
1.81Å resolution

S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3

Released:
DOI: 10.2210/pdb5elx/pdb
PDB entry 5elx coloured by chain, front view.
PDB entry 5elx coloured by chain, side view.
PDB entry 5elx coloured by chain, top view.
Source organism: Saccharomyces cerevisiae YJM789
Primary publication:
P(I) Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).
Wong EV, Cao W, Vörös J, Merchant M, Modis Y, Hackney DD, Montpetit B, De La Cruz EM
J Mol Biol 428 492-508 (2016)
PMID: 26730886

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148981 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
ATP-dependent RNA helicase DBP5 Chain: A
Molecule details ›
Chain: A
Length: 391 amino acids
Theoretical weight: 43.81 KDa
Source organism: Saccharomyces cerevisiae YJM789
Expression system: Escherichia coli
UniProt:
  • Canonical: P20449 (Residues: 91-481; Coverage: 81%)
Gene names: DBP5, RAT8, YOR046C
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases
RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
Source organism: Saccharomyces cerevisiae YJM789
Expression system: Escherichia coli

Ligands and Environments

4 bound ligands:
Ligand M2A 1 x M2A
Ligand MG 2 x MG
Ligand BEF 1 x BEF
Ligand NO3 2 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 42.082Å b: 91.751Å c: 104.521Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.208
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression.
Arul Nambi Rajan et al. (2021)
8 other articles

1 mention without citation

P(I) Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).
Wong et al. (2016)