6FSZ | pdb_00006fsz

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

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This is version 1.5 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: https://doi.org/10.1126/science.aar5428
  • Primary Citation Related Structures: 
    6FSZ, 6FT6

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 641.39 kDa 
  • Atom Count: 36,972 
  • Modeled Residue Count: 4,855 
  • Deposited Residue Count: 5,666 
  • Unique protein chains: 14
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component RRP45B [auth AA]303Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45, YDR280W, D9954.1
UniProt
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component SKI6C [auth BB]248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6, ECM20, RRP41, YGR195W, G7587
UniProt
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component RRP43D [auth CC]393Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43, YCR035C, YCR35C, YCR522
UniProt
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component RRP46E [auth DD]245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46, YGR095C
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component RRP42F [auth EE]267Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42, YDL111C
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component MTR3G [auth FF]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3, YGR158C, G6676
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component RRP40H [auth GG]242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40, YOL142W
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component RRP4I [auth HH]361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4, YHR069C
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex component CSL4J [auth II]301Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4, SKI4, YNL232W, N1154
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3K [auth JJ]1,003Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIS3, RRP44, YOL021C, O2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6L [auth KK]733Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP6, UNC733, YOR001W
EC: 3.1.13
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Exosome complex protein LRP1M [auth LL]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1, RRP47, YC1D, YHR081W
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DOB1N [auth MM]1,073Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR4, DOB1, YJL050W, J1158
EC: 3.6.4.13
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homologO [auth NN]40Saccharomyces cerevisiae, Saccharomyces cerevisiae S288C
This entity is chimeric		Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
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')A [auth 2]23Saccharomyces cerevisiae
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Reference Sequence

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  (Full details and data files)

  • 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
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references