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
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
Exosome complex component RRP45
A
304Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: D9954.1, RRP45, YDR280W
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05636

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component SKI6
B
248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM20, G7587, RRP41, SKI6, YGR195W
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46948

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
C
393Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: RRP43, YCR035C, YCR35C, YCR522
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25359

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
E
267Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP42, YDL111C
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12277

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
F
250Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: G6676, MTR3, YGR158C
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48240

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
G
242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40, YOL142W
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08285

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
H
361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4, YHR069C
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38792

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
I
301Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4, N1154, SKI4, YNL232W
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53859

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease DIS3
J
1003Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DIS3, O2197, RRP44, YOL021C
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08162

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP6
K
179Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP6, UNC733, YOR001W
EC: 3.1.13
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12149

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
D
245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46, YGR095C
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53256

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 12
MoleculeChainsLengthOrganism
RNA (45-MER)R45N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download CCD File 
G
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
C, G, H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
BR
Query on BR
Download CCD File 
A, E, F, H, I, J
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
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

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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