› 5jea

X-ray diffraction
2.65Å resolution

Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7, bound to RNA

Released:
DOI: 10.2210/pdb5jea/pdb
PDB entry 5jea coloured by chain, front view.
PDB entry 5jea coloured by chain, side view.
PDB entry 5jea coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.
Kowalinski E, Kögel A, Ebert J, Reichelt P, Stegmann E, Habermann B, Conti E
Mol Cell 63 125-34 (2016)
PMID: 27345150

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133003 (preferred)
Entry contents:
11 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (12 distinct):
Exosome complex component RRP45 Chain: A
Molecule details ›
Chain: A
Length: 305 amino acids
Theoretical weight: 34 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q05636 (Residues: 1-305; Coverage: 100%)
Gene names: D9954.1, RRP45, YDR280W
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component SKI6 Chain: B
Molecule details ›
Chain: B
Length: 249 amino acids
Theoretical weight: 27.89 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P46948 (Residues: 1-246; Coverage: 100%)
Gene names: ECM20, G7587, RRP41, SKI6, YGR195W
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP43 Chain: C
Molecule details ›
Chain: C
Length: 394 amino acids
Theoretical weight: 44.11 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P25359 (Residues: 1-394; Coverage: 100%)
Gene names: RRP43, YCR035C, YCR35C, YCR522
Sequence domains: 3' exoribonuclease family, domain 1
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP46 Chain: D
Molecule details ›
Chain: D
Length: 226 amino acids
Theoretical weight: 24.66 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53256 (Residues: 1-223; Coverage: 100%)
Gene names: RRP46, YGR095C
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP42 Chain: E
Molecule details ›
Chain: E
Length: 268 amino acids
Theoretical weight: 29.39 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12277 (Residues: 1-265; Coverage: 100%)
Gene names: RRP42, YDL111C
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component MTR3 Chain: F
Molecule details ›
Chain: F
Length: 250 amino acids
Theoretical weight: 27.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P48240 (Residues: 1-250; Coverage: 100%)
Gene names: G6676, MTR3, YGR158C
Sequence domains: 3' exoribonuclease family, domain 1
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP40 Chain: G
Molecule details ›
Chain: G
Length: 244 amino acids
Theoretical weight: 26.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08285 (Residues: 1-240; Coverage: 100%)
Gene names: RRP40, YOL142W
Sequence domains:
Structure domains:
Exosome complex component RRP4 Chain: H
Molecule details ›
Chain: H
Length: 316 amino acids
Theoretical weight: 34.6 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P38792 (Residues: 50-359; Coverage: 86%)
Gene names: RRP4, YHR069C
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Exosome complex component CSL4 Chain: I
Molecule details ›
Chain: I
Length: 295 amino acids
Theoretical weight: 31.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53859 (Residues: 1-292; Coverage: 100%)
Gene names: CSL4, N1154, SKI4, YNL232W
Sequence domains:
Exosome complex exonuclease DIS3 Chain: J
Molecule details ›
Chain: J
Length: 1005 amino acids
Theoretical weight: 114.21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08162 (Residues: 1-1001; Coverage: 100%)
Gene names: DIS3, O2197, RRP44, YOL021C
Sequence domains:
Structure domains:
Endolysin; Superkiller protein 7 Chain: K
Molecule details ›
Chain: K
Length: 279 amino acids
Theoretical weight: 31.67 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: Q08491 (Residues: 116-225; Coverage: 15%)
  • Canonical: P00720 (Residues: 1-164; Coverage: 100%)
Gene names: E, SKI7, YOR076C, YOR29-27
Sequence domains: Phage lysozyme
RNA (29-MER) Chain: R
Molecule details ›
Chain: R
Length: 46 nucleotides
Theoretical weight: 14.34 KDa

Ligands and Environments

3 bound ligands:
Ligand MPD 7 x MPD
Ligand NA 4 x NA
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 106.08Å b: 182.53Å c: 250.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.215 0.259
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Roadblocks and resolutions in eukaryotic translation.
Schuller et al. (2018)
7 more

8 mentions without citation

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors.
Zinder et al. (2017)
7 more