› 5k36

X-ray diffraction
3.1Å resolution

Structure of an eleven component nuclear RNA exosome complex bound to RNA

Released:
DOI: 10.2210/pdb5k36/pdb
PDB entry 5k36 coloured by chain, front view.
PDB entry 5k36 coloured by chain, side view.
PDB entry 5k36 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Nuclear RNA Exosome at 3.1 Å Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3.
Zinder JC, Wasmuth EV, Lima CD
Mol Cell 64 734-745 (2016)
PMID: 27818140

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150445 (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: 250 amino acids
Theoretical weight: 28.01 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: 44.06 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: 225 amino acids
Theoretical weight: 24.57 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: 269 amino acids
Theoretical weight: 29.49 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: 27.6 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: 26.99 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: 363 amino acids
Theoretical weight: 39.88 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P38792 (Residues: 1-359; Coverage: 100%)
Gene names: RRP4, YHR069C
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Exosome complex component CSL4 Chain: I
Molecule details ›
Chain: I
Length: 296 amino acids
Theoretical weight: 32.03 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 RRP6 Chain: J
Molecule details ›
Chain: J
Length: 559 amino acids
Theoretical weight: 64.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12149 (Residues: 129-684; Coverage: 76%)
Gene names: RRP6, UNC733, YOR001W
Sequence domains:
Exosome complex exonuclease DIS3 Chain: K
Molecule details ›
Chain: K
Length: 1003 amino acids
Theoretical weight: 114.06 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:
RNA (17-MER) Chains: L, M
Molecule details ›
Chains: L, M
Length: 17 nucleotides
Theoretical weight: 5.32 KDa

Ligands and Environments

3 bound ligands:
Ligand SO4 10 x SO4
Ligand GOL 7 x GOL
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 140.701Å b: 212.257Å c: 218.231Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.201 0.249
Expression system: Escherichia coli

Quick links

Citations

13 review citations

The RNA exosome and RNA exosome-linked disease.
Morton et al. (2018)
12 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