› 3rrm

X-ray diffraction
2.9Å resolution

S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp

Released:
DOI: 10.2210/pdb3rrm/pdb
PDB entry 3rrm coloured by chain, front view.
PDB entry 3rrm coloured by chain, side view.
PDB entry 3rrm 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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-148977 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
ATP-dependent RNA helicase DBP5 Chain: A
Molecule details ›
Chain: A
Length: 395 amino acids
Theoretical weight: 44.17 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20449 (Residues: 91-482; Coverage: 81%)
Gene names: DBP5, RAT8, YOR046C
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases
mRNA export factor GLE1 Chain: B
Molecule details ›
Chain: B
Length: 297 amino acids
Theoretical weight: 34.27 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12315 (Residues: 244-538; Coverage: 55%)
Gene names: BRR3, D1049, GLE1, RSS1, YDL207W
Sequence domains: GLE1-like protein
Structure domains: GLE1-like
Nucleoporin NUP159 Chain: C
Molecule details ›
Chain: C
Length: 388 amino acids
Theoretical weight: 43.04 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P40477 (Residues: 2-387; Coverage: 26%)
Gene names: NUP158, NUP159, RAT7, YIL115C
Sequence domains: Nucleoporin or Nuclear pore complex subunit NUP214=Nup159
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand ADP 1 x ADP
Ligand IHP 1 x IHP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2
Unit cell:
a: 186.912Å b: 67.982Å c: 132.392Å
α: 90° β: 127.52° γ: 90°
R-values:
R R work R free
0.23 0.228 0.261
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

51 review citations

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

9 mentions without citation

The Structure of the Nuclear Pore Complex (An Update).
Lin et al. (2019)
8 more