4IFD

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.

Makino, D.L., Baumgartner, M., Conti, E.

(2013) Nature 495: 70-75

  • DOI: 10.1038/nature11870
  • Primary Citation of Related Structures:  
    4IFD

  • PubMed Abstract: 

    • The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6 ...

    The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6. Here we crystallized an approximately 440-kilodalton complex of Saccharomyces cerevisiae Exo-10 bound to a carboxy-terminal region of Rrp6 and to an RNA duplex with a 3'-overhang of 31 ribonucleotides. The 2.8 Å resolution structure shows how RNA is funnelled into the Exo-9 channel in a single-stranded conformation by an unwinding pore. Rrp44 adopts a closed conformation and captures the RNA 3'-end that exits from the side of Exo-9. Exo-9 subunits bind RNA with sequence-unspecific interactions reminiscent of archaeal exosomes. The substrate binding and channelling mechanisms of 3'-5' RNA degradation complexes are conserved in all kingdoms of life.

    Organizational Affiliation: 

    Department of Structural Cell Biology, MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45A304Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: D9954.1, RRP45, YDR280W
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component SKI6B248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM20, G7587, RRP41, SKI6, YGR195W
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43C393Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: RRP43, YCR035C, YCR35C, YCR522
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46D245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46, YGR095C
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42E267Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP42, YDL111C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3F250Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: G6676, MTR3, YGR158C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40G242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40, YOL142W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4H361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4, YHR069C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4I301Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4, N1154, SKI4, YNL232W
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3J1,003Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DIS3, O2197, RRP44, YOL021C
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6K179Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP6, UNC733, YOR001W
EC: 3.1.13
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Entity ID: 12
MoleculeChainsLengthOrganismImage
RNA (45-MER)L [auth R]45N/A
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
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S [auth G]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
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O [auth C],
R [auth G],
U [auth H],
V [auth H],
W [auth H]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
BR
Query on BR
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AA [auth J],
BA [auth J],
M [auth A],
N [auth A],
P [auth E],
AA [auth J],
BA [auth J],
M [auth A],
N [auth A],
P [auth E],
Q [auth F],
T [auth H],
X [auth I],
Y [auth J],
Z [auth J]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
ZN
Query on ZN
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DA [auth J]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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CA [auth J]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.09α = 90
b = 107.44β = 110.63
c = 150.46γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2013-11-13
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description