Structure of the N-terminal deletion of yeast exosome component Rrp40

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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Structural and Biochemical Characterization of the Yeast Exosome Component Rrp40

Oddone, A.Lorentzen, E.Basquin, J.Gasch, A.Rybin, V.Conti, E.Sattler, M.

(2007) EMBO Rep 8: 63

  • DOI: https://doi.org/10.1038/sj.embor.7400856
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The exosome is a protein complex that is important in both degradation and 3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The structure comprises an S1 domain and an unusual KH (K homology) domain. Close packing of the S1 and KH domains is stabilized by a GxNG sequence, which is uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have very low intrinsic affinity for RNA. The affinity of an archaeal core exosome for RNA is significantly increased in the presence of the S1-KH subunit Rrp4, indicating that multiple subunits might contribute to cooperative binding of RNA substrates by the exosome.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EXOSOME COMPLEX EXONUCLEASE RRP40175Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.13
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08285 
Go to UniProtKB:  Q08285
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08285
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.51α = 90
b = 153.51β = 90
c = 153.51γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance