› 3pey

X-ray diffraction
1.4Å resolution

S. cerevisiae Dbp5 bound to RNA and ADP BeF3

Released:
DOI: 10.2210/pdb3pey/pdb
PDB entry 3pey coloured by chain, front view.
PDB entry 3pey coloured by chain, side view.
PDB entry 3pey coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export.
Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K
Nature 472 238-42 (2011)
PMID: 21441902

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-148980 (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: 395 amino acids
Theoretical weight: 44.19 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P20449 (Residues: 91-482; 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
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand ADP 1 x ADP
Ligand MG 3 x MG
Ligand BEF 1 x BEF
Ligand NO3 4 x NO3
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 42.136Å b: 92.206Å c: 104.524Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.16 0.18
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

53 review citations

From unwinding to clamping - the DEAD box RNA helicase family.
Linder et al. (2011)
52 more

6 mentions without citation

A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export.
Montpetit et al. (2011)
5 more