6H25

Human nuclear RNA exosome EXO-10-MPP6 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Distinct and evolutionary conserved structural features of the human nuclear exosome complex.

Gerlach, P.Schuller, J.M.Bonneau, F.Basquin, J.Reichelt, P.Falk, S.Conti, E.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.38686
  • Primary Citation of Related Structures:  
    6H25

  • PubMed Abstract: 

    The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP45443Homo sapiensMutation(s): 0 
Gene Names: EXOSC9PMSCL1
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Find proteins for Q06265 (Homo sapiens)
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Go to UniProtKB:  Q06265
PHAROS:  Q06265
GTEx:  ENSG00000123737 
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UniProt GroupQ06265
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP41249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4RRP41SKI6
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Find proteins for Q9NPD3 (Homo sapiens)
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Go to UniProtKB:  Q9NPD3
PHAROS:  Q9NPD3
GTEx:  ENSG00000178896 
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UniProt GroupQ9NPD3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP43278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8OIP2RRP43
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Find proteins for Q96B26 (Homo sapiens)
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PHAROS:  Q96B26
GTEx:  ENSG00000120699 
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UniProt GroupQ96B26
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP46237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5CML28RRP46
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PHAROS:  Q9NQT4
GTEx:  ENSG00000077348 
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UniProt GroupQ9NQT4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP42295Homo sapiensMutation(s): 0 
Gene Names: EXOSC7KIAA0116RRP42
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GTEx:  ENSG00000075914 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component MTR3276Homo sapiensMutation(s): 0 
Gene Names: EXOSC6MTR3
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PHAROS:  Q5RKV6
GTEx:  ENSG00000223496 
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UniProt GroupQ5RKV6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP40293Homo sapiensMutation(s): 0 
Gene Names: EXOSC3RRP40CGI-102
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PHAROS:  Q9NQT5
GTEx:  ENSG00000107371 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP4297Homo sapiensMutation(s): 0 
Gene Names: EXOSC2RRP4
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GTEx:  ENSG00000130713 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component CSL4199Homo sapiensMutation(s): 0 
Gene Names: EXOSC1CSL4CGI-108
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GTEx:  ENSG00000171311 
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UniProt GroupQ9Y3B2
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP44962Homo sapiensMutation(s): 2 
Gene Names: DIS3KIAA1008RRP44
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
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PHAROS:  Q9Y2L1
GTEx:  ENSG00000083520 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
M-phase phosphoprotein 6166Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH6MPP6
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Find proteins for Q99547 (Homo sapiens)
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GTEx:  ENSG00000135698 
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Entity ID: 12
MoleculeChains LengthOrganismImage
U44 ssRNAL [auth R]44synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationALTF 1008-2015
European CommissionERC-2016-ADG 740329 EXORICO
German Research FoundationSFB646, SFB1035, GRK1721
Louis-Jeantet Foundation--
Max Planck Society--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations