5VZJ

STRUCTURE OF A TWELVE COMPONENT MPP6-NUCLEAR RNA EXOSOME COMPLEX BOUND TO RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase.

Wasmuth, E.V.Zinder, J.C.Zattas, D.Das, M.Lima, C.D.

(2017) Elife 6

  • DOI: 10.7554/eLife.29062
  • Primary Citation of Related Structures:  
    5VZJ

  • PubMed Abstract: 
  • Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the ex ...

    Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the exoribonuclease Rrp6 and recruits Mtr4, but it is less clear if these cofactors work together. Using biochemistry with Saccharomyces cerevisiae proteins, we show that Rrp47 and Mpp6 stimulate exosome-mediated RNA decay, albeit with unique dependencies on elements within the nuclear exosome. Mpp6-exosomes can recruit Mtr4, while Mpp6 and Rrp47 each contribute to Mtr4-dependent RNA decay, with maximal Mtr4-dependent decay observed with both cofactors. The 3.3 Å structure of a twelve-subunit nuclear Mpp6 exosome bound to RNA shows the central region of Mpp6 bound to the exosome core, positioning its Mtr4 recruitment domain next to Rrp6 and the exosome central channel. Genetic analysis reveals interactions that are largely consistent with our model.


    Organizational Affiliation

    Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States.



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 SKI6B250Saccharomyces 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
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46D225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42E269Saccharomyces cerevisiae S288CMutation(s): 0 
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): 0 
Gene Names: MTR3YGR158CG6676
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40G244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
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Exosome complex exonuclease DIS3K1003Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DIS3RRP44YOL021CO2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
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M-phase phosphoprotein 6 homologL42Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP6YNR024WN3230
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  • Entity ID: 13
    MoleculeChainsLengthOrganismImage
    RNA (11-MER)M11Homo sapiens
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    • Entity ID: 14
      MoleculeChainsLengthOrganismImage
      RNA (19-MER)N19Homo sapiens
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.30 Å
      • R-Value Free: 0.266 
      • R-Value Work: 0.217 
      • R-Value Observed: 0.219 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 141.09α = 90
      b = 213.592β = 90
      c = 225.909γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data reduction
      SCALEPACKdata scaling
      PHASERphasing
      PHENIXrefinement
      PDB_EXTRACTdata extraction

      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
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118080
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF31GM097910
      Howard Hughes Medical Institute (HHMI)United States--
      National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA008748

      Revision History 

      • Version 1.0: 2017-08-02
        Type: Initial release
      • Version 1.1: 2017-08-09
        Changes: Database references
      • Version 1.2: 2019-11-20
        Changes: Author supporting evidence