5C0X

Structure of a 12-subunit nuclear exosome complex bound to structured RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.295 

Starting Models: experimental
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This is version 1.4 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: https://doi.org/10.1038/nature14865
  • Primary Citation of Related Structures:  
    5C0W, 5C0X, 5C0Y

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP45305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
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UniProt GroupQ05636
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component SKI6248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
UniProt
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UniProt GroupP46948
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP43394Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: RRP43YCR035CYCR35CYCR522
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP46245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
UniProt
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UniProt GroupP53256
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP42267Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP42YDL111C
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UniProt GroupQ12277
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component MTR3250Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: MTR3YGR158CG6676
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP40243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
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UniProt GroupQ08285
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP4361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
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UniProt GroupP38792
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component CSL4295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS31,003Saccharomyces 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
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6695Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
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Entity ID: 12
MoleculeChains LengthOrganismImage
RNA syntheticL [auth R]45synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth J]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.295 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.15α = 90
b = 177.39β = 90
c = 299.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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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  (Full details and data files)

  • 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: Advisory, Author supporting evidence, Derived calculations
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description