› 3m7n

X-ray diffraction
2.4Å resolution

archaeoglobus fulgidus exosome with RNA bound to the active site

Released:
DOI: 10.2210/pdb3m7n/pdb
PDB entry 3m7n coloured by chain, front view.
PDB entry 3m7n coloured by chain, side view.
PDB entry 3m7n coloured by chain, top view.
Source organism: Archaeoglobus fulgidus
Primary publication:
Quantitative analysis of processive RNA degradation by the archaeal RNA exosome.
Hartung S, Niederberger T, Hartung M, Tresch A, Hopfner KP
Nucleic Acids Res 38 5166-76 (2010)
PMID: 20392821

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128163 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
Exosome complex component Csl4 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 179 amino acids
Theoretical weight: 19.63 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O30033 (Residues: 1-179; Coverage: 100%)
Gene names: AF_0206, csl4
Sequence domains:
Structure domains:
Exosome complex component Rrp41 Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 258 amino acids
Theoretical weight: 28.86 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O29757 (Residues: 1-258; Coverage: 100%)
Gene names: AF_0493, rrp41
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component Rrp42 Chains: G, H, I
Molecule details ›
Chains: G, H, I
Length: 259 amino acids
Theoretical weight: 28.68 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O29756 (Residues: 1-259; Coverage: 100%)
Gene names: AF_0494, rrp42
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
5'-R(*C*UP*CP*CP*CP*C)-3' Chains: X, Y, Z
Molecule details ›
Chains: X, Y, Z
Length: 6 nucleotides
Theoretical weight: 1.79 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P4322
Unit cell:
a: 138.268Å b: 138.268Å c: 262.273Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.27 0.197 0.256
Expression system: Escherichia coli

Quick links

Citations

5 review citations

RNA decay machines: the exosome.
Chlebowski et al. (2013)
4 more

1 mention without citation

Structure based approach for understanding organism specific recognition of protein-RNA complexes.
Nagarajan et al. (2015)