4WFD

Structure of the Rrp6-Rrp47-Mtr4 interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report



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: 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 fun ...

    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 p.j.mitchell@sheffield.ac.uk conti@biochem.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6ADG115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12149 
Go to UniProtKB:  Q12149
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex protein LRP1BEH103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1RRP47YC1DYHR081W
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38801 
Go to UniProtKB:  P38801
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DOB1CFI20Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR4DOB1YJL050WJ1158
EC: 3.6.4.13
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47047 
Go to UniProtKB:  P47047
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YT3
Query on YT3

Download CCD File 
A, B, C, D, E, F, G, I
YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 3 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.745α = 90
b = 142.745β = 90
c = 63.45γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Cootmodel building
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-09-14 
  • Released Date: 2014-10-29 
  • Deposition Author(s): Schuch, B., Conti, E.

Funding OrganizationLocationGrant Number
European Research CouncilAdvanced Investigator Grant 294371
Marie CurieITN RNPnet
German Research FoundationGermanyDFG SFB646, SFB1035, GRK1721, FOR1680, CIPSM

Revision History 

  • 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