› 4oo1

X-ray diffraction
3.3Å resolution

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

Released:
DOI: 10.2210/pdb4oo1/pdb
PDB entry 4oo1 coloured by chain, front view.
PDB entry 4oo1 coloured by chain, side view.
PDB entry 4oo1 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA.
Wasmuth EV, Januszyk K, Lima CD
Nature 511 435-9 (2014)
PMID: 25043052

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-150446 (preferred)
Entry contents:
10 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (11 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:
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 BL21(DE3)
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 BL21(DE3)
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 BL21(DE3)
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 BL21(DE3)
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 BL21(DE3)
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 BL21(DE3)
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 BL21(DE3)
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 BL21(DE3)
UniProt:
  • Canonical: P53859 (Residues: 1-292; Coverage: 100%)
Gene names: CSL4, N1154, SKI4, YNL232W
Sequence domains:
Structure domains:
Exosome complex exonuclease RRP6 Chain: J
Molecule details ›
Chain: J
Length: 560 amino acids
Theoretical weight: 64.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12149 (Residues: 129-685; Coverage: 76%)
Gene names: RRP6, UNC733, YOR001W
Sequence domains:
Structure domains:
POLY A RNA Chain: S
Molecule details ›
Chain: S
Length: 24 nucleotides
Theoretical weight: 7.86 KDa

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand MPD 1 x MPD
Ligand MES 1 x MES
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21212
Unit cell:
a: 193.292Å b: 200.083Å c: 97.405Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.227 0.265
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

21 review citations

Shedding light on the cell biology of extracellular vesicles.
van Niel et al. (2018)
20 more

8 mentions without citation

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA.
Wasmuth et al. (2014)
7 more