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: 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 ...

    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 RRP45305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45, YDR280W, D9954.1
UniProt
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UniProt GroupQ05636
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component SKI6250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6, ECM20, RRP41, YGR195W, G7587
UniProt
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UniProt GroupP46948
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43, YCR035C, YCR35C, YCR522
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46, YGR095C
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42269Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42, YDL111C
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3, YGR158C, G6676
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40, YOL142W
UniProt
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UniProt GroupQ08285
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4363Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4, YHR069C
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4, SKI4, YNL232W, N1154
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6559Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP6, UNC733, YOR001W
EC: 3.1.13
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS31,003Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DIS3, RRP44, YOL021C, O2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt
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Entity ID: 12
MoleculeChainsLengthOrganismImage
RNA (17-MER)L [auth M],
M [auth L]		17synthetic construct
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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]
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]
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

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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