6FSZ

Structure of the nuclear RNA exosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the nuclear exosome captured on a maturing preribosome.

Schuller, J.M.Falk, S.Fromm, L.Hurt, E.Conti, E.

(2018) Science 360: 219-222

  • DOI: 10.1126/science.aar5428
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60 ...

    The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60 S ) during 7 S -to-5.8 S rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 S particle, which harbors the 5.8 S rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 S rRNA, captures the 3' extension of the 5.8 S rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 S substrate to process rRNA during ribosome maturation.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute (MPI) for Biochemistry, Munich, Germany. conti@biochem.mpg.de ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
AA
303Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05636
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component SKI6
BB
248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46948
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
DD
245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53256
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
EE
267Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42YDL111C
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12277
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
GG
242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08285
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
HH
361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP6
KK
733Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Exosome complex protein LRP1
LL
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1RRP47YC1DYHR081W
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DOB1
MM
1073Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR4DOB1YJL050WJ1158
EC: 3.6.4.13
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
II
301Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease DIS3
JJ
1003Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIS3RRP44YOL021CO2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
NN
40Saccharomyces cerevisiaeSaccharomyces cerevisiae S288C
This entity is chimeric
Mutation(s): 0 
Find proteins for P53725 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
CC
393Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25359
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
FF
250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3YGR158CG6676
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48240
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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')223Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERCBelgiumEXORICO

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Other, Source and taxonomy
  • Version 1.4: 2019-12-18
    Changes: Source and taxonomy