› 4ifd

X-ray diffraction
2.8Å resolution

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Released:
DOI: 10.2210/pdb4ifd/pdb
PDB entry 4ifd coloured by chain, front view.
PDB entry 4ifd coloured by chain, side view.
PDB entry 4ifd coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
Makino DL, Baumgärtner M, Conti E
Nature 495 70-5 (2013)
PMID: 23376952

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-150443 (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: 304 amino acids
Theoretical weight: 33.87 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q05636 (Residues: 2-305; 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: 248 amino acids
Theoretical weight: 27.79 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: 393 amino acids
Theoretical weight: 43.98 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P25359 (Residues: 2-394; 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: 245 amino acids
Theoretical weight: 26.91 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: 267 amino acids
Theoretical weight: 29.29 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: 27.56 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: 242 amino acids
Theoretical weight: 26.78 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: 361 amino acids
Theoretical weight: 39.71 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: 301 amino acids
Theoretical weight: 32.81 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:
Structure domains:
Exosome complex exonuclease DIS3 Chain: J
Molecule details ›
Chain: J
Length: 1003 amino acids
Theoretical weight: 113.98 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:
Exosome complex exonuclease RRP6 Chain: K
Molecule details ›
Chain: K
Length: 179 amino acids
Theoretical weight: 19.88 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12149 (Residues: 518-693; Coverage: 24%)
Gene names: RRP6, UNC733, YOR001W
Structure domains:
RNA (45-MER) Chain: R
Molecule details ›
Chain: R
Length: 45 nucleotides
Theoretical weight: 14.05 KDa

Ligands and Environments

5 bound ligands:
Ligand BR 10 x BR
Ligand GOL 5 x GOL
Ligand MES 1 x MES
Ligand MG 1 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 154.09Å b: 107.44Å c: 150.46Å
α: 90° β: 110.63° γ: 90°
R-values:
R R work R free
0.185 0.182 0.224
Expression system: Escherichia coli

Quick links

Citations

39 review citations

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

28 mentions without citation

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