› 4wfd

X-ray diffraction
2.4Å resolution

Structure of the Rrp6-Rrp47-Mtr4 interaction

Released:
DOI: 10.2210/pdb4wfd/pdb
PDB entry 4wfd coloured by chain, front view.
PDB entry 4wfd coloured by chain, side view.
PDB entry 4wfd coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.
Schuch B, Feigenbutz M, Makino DL, Falk S, Basquin C, Mitchell P, Conti E
EMBO J 33 2829-46 (2014)
PMID: 25319414

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-153725 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Exosome complex exonuclease RRP6 Chains: A, D, G
Molecule details ›
Chains: A, D, G
Length: 115 amino acids
Theoretical weight: 12.86 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12149 (Residues: 1-111; Coverage: 15%)
Gene names: RRP6, UNC733, YOR001W
Sequence domains: PMC2NT (NUC016) domain
Exosome complex protein LRP1 Chains: B, E, H
Molecule details ›
Chains: B, E, H
Length: 103 amino acids
Theoretical weight: 12.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P38801 (Residues: 1-103; Coverage: 56%)
Gene names: LRP1, RRP47, YC1D, YHR081W
Sequence domains: Sas10/Utp3/C1D family
ATP-dependent RNA helicase DOB1 Chains: C, F, I
Molecule details ›
Chains: C, F, I
Length: 20 amino acids
Theoretical weight: 2.31 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
UniProt:
  • Canonical: P47047 (Residues: 1-19; Coverage: 2%)
Gene names: DOB1, J1158, MTR4, YJL050W

Ligands and Environments

1 bound ligand:
Ligand YT3 22 x YT3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P312
Unit cell:
a: 142.745Å b: 142.745Å c: 63.45Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.203 0.201 0.243
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

18 review citations

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

4 mentions without citation

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