4IFD

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.805 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 

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

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
A
304Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP45
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05636
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component SKI6
B
248Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI6 (ECM20, RRP41)
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46948
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
C
393Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: RRP43
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25359
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
D
245Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP46
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53256
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
E
267Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: RRP42
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12277
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
F
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: MTR3
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48240
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
G
242Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP40
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08285
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
H
361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP4
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38792
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
I
301Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSL4 (SKI4)
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53859
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease DIS3
J
1003Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: DIS3 (RRP44)
EC: 3.1.13.-, 3.1.26.-
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: DIS3
Go to UniProtKB:  Q08162
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP6
K
179Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP6 (UNC733)
EC: 3.1.13.-
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12149
Entity ID: 12
MoleculeChainsLengthOrganism
RNA (45-MER)R45N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
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Download CCD File 
J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL
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Download CCD File 
C, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR
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Download CCD File 
A, E, F, H, I, J
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG
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J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES
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G
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.805 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 154.090α = 90.00
b = 107.440β = 110.63
c = 150.460γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
RemDAqdata collection
XSCALEdata scaling
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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