› 2po0

X-ray diffraction
2.3Å resolution

Crystal structure of the P. abyssi exosome RNase PH ring complexed with ADP in double conformation

Released:
DOI: 10.2210/pdb2po0/pdb
PDB 2po0 coloured by chain and viewed from the front.
PDB 2po0 coloured by chain and viewed from the side.
PDB 2po0 coloured by chain and viewed from the top.
Source organism: Pyrococcus abyssi
Primary publication:
Insights into the mechanism of progressive RNA degradation by the archaeal exosome.
Navarro MV, Oliveira CC, Zanchin NI, Guimar��es BG
J. Biol. Chem. 283 14120-31 (2008)
PMID: 18353775

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Exosome complex component Rrp41 Chain: A
Molecule details ›
Chain: A
Length: 249 amino acids
Theoretical weight: 27.72 KDa
Source organism: Pyrococcus abyssi
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9V119 (Residues: 1-249; Coverage: 100%)
Gene names: PAB0420, PYRAB06100, rrp41
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component Rrp42 Chain: B
Molecule details ›
Chain: B
Length: 277 amino acids
Theoretical weight: 30.27 KDa
Source organism: Pyrococcus abyssi
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9V118 (Residues: 1-274; Coverage: 100%)
Gene names: PAB0421, PYRAB06110, rrp42
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain

Ligands and Environments

2 bound ligands:
Ligand ADP 1 x ADP
Ligand MPD 3 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE D03B-MX1
Spacegroup: P321
Unit cell:
a: 94.2Å b: 94.2Å c: 127.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.19 0.243
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)
8 more

1 mention without citation

Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
Nurmohamed et al. (2009)