5C0W

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.277 

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This is version 1.3 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 repo ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45A305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component SKI6B248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43C394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46D245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42E267Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP42YDL111C
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3F250Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: MTR3YGR158CG6676
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40G243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4H361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4I295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3J1004Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DIS3RRP44YOL021CO2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6K695Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex protein LRP1L184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1RRP47YC1DYHR081W
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 13
    MoleculeChainsLengthOrganismImage
    RNA syntheticN, R18synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    J
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 4.60 Å
    • R-Value Free: 0.284 
    • R-Value Work: 0.271 
    • R-Value Observed: 0.277 
    • Space Group: P 32 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 195.38α = 90
    b = 195.38β = 90
    c = 463.65γ = 120
    Software Package:
    Software NamePurpose
    XDSdata reduction
    XSCALEdata scaling
    PHASERphasing
    PHENIXrefinement
    Cootmodel building
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Max Planck SocietyGermany--
    European CommissionGermanyERC 294371
    European CommissionGermanyMarie Curie ITN RNPnet
    German Research FoundationGermanySFB646, SFB1035, GRK1721, FOR1680, CIPSM
    Louis JeantetGermany--

    Revision History 

    • Version 1.0: 2015-07-29
      Type: Initial release
    • Version 1.1: 2015-08-12
      Changes: Database references
    • Version 1.2: 2017-09-06
      Changes: Author supporting evidence
    • Version 1.3: 2019-02-20
      Changes: Advisory, Data collection, Derived calculations