5K36

Structure of an eleven component nuclear RNA exosome complex bound to RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3.

Zinder, J.C.Wasmuth, E.V.Lima, C.D.

(2016) Mol Cell 64: 734-745

  • DOI: 10.1016/j.molcel.2016.09.038
  • Primary Citation of Related Structures:  
    5K36

  • PubMed Abstract: 
  • The eukaryotic RNA exosome is an essential and conserved 3'-to-5' exoribonuclease complex that degrades or processes nearly every class of cellular RNA. The nuclear RNA exosome includes a 9-subunit non-catalytic core that binds Rrp44 (Dis3) and Rrp6 subunits to modulate their processive and distributive 3'-to-5' exoribonuclease activities, respectively ...

    The eukaryotic RNA exosome is an essential and conserved 3'-to-5' exoribonuclease complex that degrades or processes nearly every class of cellular RNA. The nuclear RNA exosome includes a 9-subunit non-catalytic core that binds Rrp44 (Dis3) and Rrp6 subunits to modulate their processive and distributive 3'-to-5' exoribonuclease activities, respectively. Here we utilize an engineered RNA with two 3' ends to obtain a crystal structure of an 11-subunit nuclear exosome bound to RNA at 3.1 Å. The structure reveals an extended RNA path to Rrp6 that penetrates into the non-catalytic core; contacts between the non-catalytic core and Rrp44, which inhibit exoribonuclease activity; and features of the Rrp44 exoribonuclease site that support its ability to degrade 3' phosphate RNA substrates. Using reconstituted exosome complexes, we show that 3' phosphate RNA is not a substrate for Rrp6 but is readily degraded by Rrp44 in the nuclear exosome.


    Organizational Affiliation

    Structural Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA. Electronic address: limac@mskcc.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45A305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
UniProt
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component SKI6B250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43C394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46D225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42E269Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42YDL111C
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3F250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3YGR158CG6676
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40G244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4H363Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4I296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6J559Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3K1003Saccharomyces 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: 12
    MoleculeChainsLengthOrganismImage
    RNA (17-MER)M [auth L], L [auth M]17synthetic construct
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    AA [auth K] , BA [auth K] , EA [auth M] , N [auth A] , R [auth B] , T [auth D] , U [auth E] , V [auth F] , 
    AA [auth K], BA [auth K], EA [auth M], N [auth A], R [auth B], T [auth D], U [auth E], V [auth F], W [auth G], Y [auth I]
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    GOL
    Query on GOL

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    CA [auth K], DA [auth K], O [auth A], P [auth A], Q [auth A], S [auth B], X [auth H]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    Z [auth K]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.10 Å
    • R-Value Free: 0.249 
    • R-Value Work: 0.201 
    • R-Value Observed: 0.203 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 140.701α = 90
    b = 212.257β = 90
    c = 218.231γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    SCALEPACKdata scaling
    PHASERphasing
    PDB_EXTRACTdata extraction
    Cootmodel building
    HKL-2000data reduction

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079196
    Howard Hughes Medical Institute (HHMI)United States--

    Revision History  (Full details and data files)

    • Version 1.0: 2016-11-02
      Type: Initial release
    • Version 1.1: 2016-12-07
      Changes: Database references
    • Version 1.2: 2017-09-20
      Changes: Author supporting evidence, Database references
    • Version 1.3: 2017-11-01
      Changes: Author supporting evidence
    • Version 1.4: 2019-11-20
      Changes: Author supporting evidence