4WFD

Structure of the Rrp6-Rrp47-Mtr4 interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 

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: 10.15252/embj.201488757
  • Primary Citation of Related Structures:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP6
A, D, G
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP6 (UNC733)
EC: 3.1.13.-
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12149
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex protein LRP1
B, E, H
103Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LRP1 (RRP47, YC1D)
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LRP1
Go to UniProtKB:  P38801
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DOB1
C, F, I
20Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MTR4 (DOB1)
EC: 3.6.4.13
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47047
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YT3
Query on YT3

Download SDF File 
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: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • Space Group: P 3 1 2
Unit Cell:
Length (Å)Angle (°)
a = 142.745α = 90.00
b = 142.745β = 90.00
c = 63.450γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

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

Funding OrganizationCountryGrant 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
    Type: Database references
  • Version 2.0: 2017-09-06
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations, Refinement description