PDBe 4ifd

X-ray diffraction
2.8Å resolution

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

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 12-mer (preferred)
Entry contents:
11 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (12 distinct):
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: Exosome component EXOSC1/CSL4
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 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:
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 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: KH domain
Structure domains: Nucleic acid-binding proteins
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
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
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 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 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:
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
RNA (45-MER) Chain: R
Molecule details ›
Chain: R
Length: 45 nucleotides
Theoretical weight: 14.05 KDa

Ligands and Environments


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