› 2hbm

X-ray diffraction
2.7Å resolution

Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn, Zn, and UMP

Released:
DOI: 10.2210/pdb2hbm/pdb
PDB entry 2hbm coloured by chain, front view.
PDB entry 2hbm coloured by chain, side view.
PDB entry 2hbm coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain.
Midtgaard SF, Assenholt J, Jonstrup AT, Van LB, Jensen TH, Brodersen DE
Proc Natl Acad Sci U S A 103 11898-903 (2006)
PMID: 16882719

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171303 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Exosome complex exonuclease RRP6 Chain: A
Molecule details ›
Chain: A
Length: 410 amino acids
Theoretical weight: 47.68 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12149 (Residues: 129-536; Coverage: 56%)
Gene names: RRP6, UNC733, YOR001W
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MN 1 x MN
Ligand U 1 x U
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR591
Spacegroup: P3121
Unit cell:
a: 110.577Å b: 110.577Å c: 79.33Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.22 0.286
Expression system: Escherichia coli

Quick links

Citations

19 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
18 more

2 mentions without citation

Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain.
Midtgaard et al. (2006)
1 more