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 

Starting Models: experimental
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This is version 1.5 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: https://doi.org/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. 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

    Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Structural Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP45305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
UniProt
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UniProt GroupQ05636
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component SKI6250Saccharomyces 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): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP46225Saccharomyces 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 RRP42269Saccharomyces cerevisiae S288CMutation(s): 0 
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): 0 
Gene Names: MTR3YGR158CG6676
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP40244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
UniProt
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UniProt GroupQ08285
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP4363Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
UniProt
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UniProt GroupP38792
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component CSL4296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6559Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
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Entity ID: 11
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)
UniProt
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Entity ID: 12
MoleculeChains LengthOrganismImage
RNA (17-MER)L [auth M],
M [auth L]
17synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / 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]
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
GOL
Query on GOL

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CA [auth K]
DA [auth K]
O [auth A]
P [auth A]
Q [auth A]
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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Z [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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

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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
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description