4WFC

Structure of the Rrp6-Rrp47 interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.

Schuch, B.Feigenbutz, M.Makino, D.L.Falk, S.Basquin, C.Mitchell, P.Conti, E.

(2014) EMBO J 33: 2829-2846

  • DOI: https://doi.org/10.15252/embj.201488757
  • Primary Citation of Related Structures:  
    4WFC, 4WFD

  • PubMed Abstract: 

    The exosome is a conserved multi-subunit ribonuclease complex that functions in 3' end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10-subunit core complex of the exosome (Exo-10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo-10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N-terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N-terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C-terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6-Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.


  • Organizational Affiliation

    Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6
A, C, E
115Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
UniProt
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12149 
Go to UniProtKB:  Q12149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12149
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex protein LRP1
B, D, F
133Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LRP1RRP47YC1DYHR081W
UniProt
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38801 
Go to UniProtKB:  P38801
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38801
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.397α = 90
b = 98.397β = 90
c = 208.018γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilAdvanced Investigator Grant 294371
Marie CurieITN RNPnet
German Research FoundationGermanySFB646, SFB1035, GRK1721, FOR1680, CIPSM

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 2.0: 2017-09-06
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations, Refinement description