5C0Y

Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RNA degradation paths in a 12-subunit nuclear exosome complex.

Makino, D.L.Schuch, B.Stegmann, E.Baumgartner, M.Basquin, C.Conti, E.

(2015) Nature 524: 54-58

  • DOI: 10.1038/nature14865
  • Primary Citation of Related Structures:  
    5C0W, 5C0Y, 5C0X

  • PubMed Abstract: 
  • The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report t ...

    The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report the crystal structures of a yeast nuclear exosome containing the 9-subunit core, the 3'-5' RNases Rrp44 and Rrp6, and the obligate Rrp6-binding partner Rrp47 in complex with different RNAs. The combined structural and biochemical data of this 12-subunit complex reveal how a single-stranded RNA can reach the Rrp44 or Rrp6 active sites directly or can bind Rrp6 and be threaded via the central channel towards the distal RNase Rrp44. When a bulky RNA is stalled at the entrance of the channel, Rrp6-Rrp47 swings open. The results suggest how the same molecular machine can coordinate processive degradation and partial trimming in an RNA-dependent manner by a concerted swinging mechanism of the two RNase subunits.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6 AB402Saccharomyces cerevisiae S288CMutation(s): 1 
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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    poly U RNAC, D15synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    B
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.180 
    • R-Value Work: 0.148 
    • R-Value Observed: 0.151 
    • Space Group: P 31
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 110.186α = 90
    b = 110.186β = 90
    c = 78.883γ = 120
    Software Package:
    Software NamePurpose
    XDSdata reduction
    Aimlessdata scaling
    PHASERphasing
    PHENIXrefinement
    Cootmodel building
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2015-06-12 
    • Released Date: 2015-08-05 
    • Deposition Author(s): Schuch, B., Conti, E.

    Funding OrganizationLocationGrant Number
    European Research CouncilGermanyAdvanced Investigator Grant 294371
    Marie CurieGermanyITN RNPnet
    German Research FoundationGermanySFB646, SFB1035, GRK1721, FOR1680 and CIPSM
    Louis Jeantet FoundationSwitzerland--

    Revision History 

    • Version 1.0: 2015-08-05
      Type: Initial release
    • Version 1.1: 2015-08-12
      Changes: Database references
    • Version 1.2: 2017-09-06
      Changes: Author supporting evidence