4OO1

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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This is version 1.2 of the entry. See complete history


Literature

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA.

Wasmuth, E.V.Januszyk, K.Lima, C.D.

(2014) Nature 511: 435-439

  • DOI: 10.1038/nature13406
  • Primary Citation of Related Structures:  
    4OO1

  • PubMed Abstract: 
  • The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominen ...

    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.


    Organizational Affiliation

    1] Structural Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA [2] Howard Hughes Medical Institute, 1275 York Avenue, New York, New York 10065, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45A305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: D9954.1RRP45YDR280W
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: ECM20G7587RRP41SKI6YGR195W
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
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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: G6676MTR3YGR158C
EC: 3.1.13
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
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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: CSL4N1154SKI4YNL232W
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6J560Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
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  • Reference Sequence
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Entity ID: 11
MoleculeChainsLengthOrganismImage
POLY A RNAS24N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
G
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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E
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PO4
Query on PO4

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I, S
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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E, S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.292α = 90
b = 200.083β = 90
c = 97.405γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description