5C0X

Structure of a 12-subunit nuclear exosome complex bound to structured RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.812 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

RNA degradation paths in a 12-subunit nuclear exosome complex.

Makino, D.L.Schuch, B.Stegmann, E.Baumgartner, M.Basquin, C.Conti, E.

(2015) Nature 524: 54-58

  • DOI: 10.1038/nature14865
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we repo ...

    The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report the crystal structures of a yeast nuclear exosome containing the 9-subunit core, the 3'-5' RNases Rrp44 and Rrp6, and the obligate Rrp6-binding partner Rrp47 in complex with different RNAs. The combined structural and biochemical data of this 12-subunit complex reveal how a single-stranded RNA can reach the Rrp44 or Rrp6 active sites directly or can bind Rrp6 and be threaded via the central channel towards the distal RNase Rrp44. When a bulky RNA is stalled at the entrance of the channel, Rrp6-Rrp47 swings open. The results suggest how the same molecular machine can coordinate processive degradation and partial trimming in an RNA-dependent manner by a concerted swinging mechanism of the two RNase subunits.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
A
305Saccharomyces 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
394Saccharomyces 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
243Saccharomyces 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
295Saccharomyces 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
695Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
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 syntheticR45synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.812 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.295 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.150α = 90.00
b = 177.390β = 90.00
c = 299.900γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European CommissionGermanyERC 294371
European CommissionGermanyMarie Curie ITN RNPnet
German Research FoundationGermanySFB646, SFB1035, GRK1721, FOR1680, CIPSM
Louis JeantetGermany--

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Advisory, Author supporting evidence, Derived calculations