› 5c0w

X-ray diffraction
4.6Å resolution

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

Released:
DOI: 10.2210/pdb5c0w/pdb
PDB entry 5c0w coloured by chain, front view.
PDB entry 5c0w coloured by chain, side view.
PDB entry 5c0w coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
RNA degradation paths in a 12-subunit nuclear exosome complex.
Makino DL, Schuch B, Stegmann E, Baumgärtner M, Basquin C, Conti E
Nature 524 54-8 (2015)
PMID: 26222026

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150439 (preferred)
Entry contents:
12 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (13 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 BL21(DE3)
UniProt:
  • Canonical: Q05636 (Residues: 1-305; Coverage: 100%)
Gene names: D9954.1, RRP45, YDR280W
Sequence domains:
Exosome complex component SKI6 Chain: B
Molecule details ›
Chain: B
Length: 248 amino acids
Theoretical weight: 27.79 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46948 (Residues: 1-246; Coverage: 100%)
Gene names: ECM20, G7587, RRP41, SKI6, YGR195W
Sequence domains:
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 BL21(DE3)
UniProt:
  • Canonical: P25359 (Residues: 1-394; Coverage: 100%)
Gene names: RRP43, YCR035C, YCR35C, YCR522
Sequence domains: 3' exoribonuclease family, domain 1
Exosome complex component RRP46 Chain: D
Molecule details ›
Chain: D
Length: 245 amino acids
Theoretical weight: 26.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P53256 (Residues: 1-223; Coverage: 100%)
Gene names: RRP46, YGR095C
Sequence domains:
Exosome complex component RRP42 Chain: E
Molecule details ›
Chain: E
Length: 267 amino acids
Theoretical weight: 29.29 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12277 (Residues: 1-265; Coverage: 100%)
Gene names: RRP42, YDL111C
Exosome complex component MTR3 Chain: F
Molecule details ›
Chain: F
Length: 250 amino acids
Theoretical weight: 27.56 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P48240 (Residues: 1-250; Coverage: 100%)
Gene names: G6676, MTR3, YGR158C
Sequence domains: 3' exoribonuclease family, domain 1
Exosome complex component RRP40 Chain: G
Molecule details ›
Chain: G
Length: 243 amino acids
Theoretical weight: 26.88 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08285 (Residues: 1-240; Coverage: 100%)
Gene names: RRP40, YOL142W
Sequence domains:
Exosome complex component RRP4 Chain: H
Molecule details ›
Chain: H
Length: 361 amino acids
Theoretical weight: 39.71 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38792 (Residues: 1-359; Coverage: 100%)
Gene names: RRP4, YHR069C
Sequence domains:
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 BL21(DE3)
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: 1004 amino acids
Theoretical weight: 114.08 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08162 (Residues: 1-1001; Coverage: 100%)
Gene names: DIS3, O2197, RRP44, YOL021C
Sequence domains:
Exosome complex exonuclease RRP6 Chain: K
Molecule details ›
Chain: K
Length: 695 amino acids
Theoretical weight: 79.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12149 (Residues: 1-693; Coverage: 95%)
Gene names: RRP6, UNC733, YOR001W
Sequence domains:
Exosome complex protein LRP1 Chain: L
Molecule details ›
Chain: L
Length: 184 amino acids
Theoretical weight: 21.09 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38801 (Residues: 1-184; Coverage: 100%)
Gene names: LRP1, RRP47, YC1D, YHR081W
Sequence domains: Sas10/Utp3/C1D family
RNA synthetic Chains: N, R
Molecule details ›
Chains: N, R
Length: 18 nucleotides
Theoretical weight: 5.81 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P3221
Unit cell:
a: 195.38Å b: 195.38Å c: 463.65Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.277 0.271 0.284
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

The regulation and functions of the nuclear RNA exosome complex.
Kilchert et al. (2016)
15 more

12 mentions without citation

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