6D6Q

Human nuclear exosome-MTR4 RNA complex - overall reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.

Weick, E.M.Puno, M.R.Januszyk, K.Zinder, J.C.DiMattia, M.A.Lima, C.D.

(2018) Cell 173: 1663

  • DOI: 10.1016/j.cell.2018.05.041
  • Primary Citation of Related Structures:  
    6D6Q, 6D6R

  • PubMed Abstract: 
  • The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Sch ...

    The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.


    Organizational Affiliation

    Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA. Electronic address: limac@mskcc.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45A473Homo sapiensMutation(s): 0 
Gene Names: EXOSC9PMSCL1
Find proteins for Q06265 (Homo sapiens)
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PHAROS  Q06265
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP41B249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4RRP41SKI6
Find proteins for Q9NPD3 (Homo sapiens)
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PHAROS  Q9NPD3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43C278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8OIP2RRP43
Find proteins for Q96B26 (Homo sapiens)
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PHAROS  Q96B26
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46D237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5CML28RRP46
Find proteins for Q9NQT4 (Homo sapiens)
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PHAROS  Q9NQT4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42E293Homo sapiensMutation(s): 0 
Gene Names: EXOSC7KIAA0116RRP42
Find proteins for Q15024 (Homo sapiens)
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PHAROS  Q15024
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3F272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6MTR3
Find proteins for Q5RKV6 (Homo sapiens)
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PHAROS  Q5RKV6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40G277Homo sapiensMutation(s): 1 
Gene Names: EXOSC3RRP40CGI-102
Find proteins for Q9NQT5 (Homo sapiens)
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PHAROS  Q9NQT5
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4H296Homo sapiensMutation(s): 0 
Gene Names: EXOSC2RRP4
Find proteins for Q13868 (Homo sapiens)
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PHAROS  Q13868
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4I197Homo sapiensMutation(s): 0 
Gene Names: EXOSC1CSL4CGI-108
Find proteins for Q9Y3B2 (Homo sapiens)
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PHAROS  Q9Y3B2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome component 10J761Homo sapiensMutation(s): 1 
Gene Names: EXOSC10PMSCLPMSCL2RRP6
EC: 3.1.13
Find proteins for Q01780 (Homo sapiens)
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PHAROS  Q01780
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP44K960Homo sapiensMutation(s): 4 
Gene Names: DIS3KIAA1008RRP44
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for Q9Y2L1 (Homo sapiens)
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PHAROS  Q9Y2L1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
M-phase phosphoprotein 6L162Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH6MPP6
Find proteins for Q99547 (Homo sapiens)
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PHAROS  Q99547
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome RNA helicase MTR4M1045Homo sapiensMutation(s): 0 
Gene Names: MTREXDOB1KIAA0052MTR4SKIV2L2
EC: 3.6.4.13
Find proteins for P42285 (Homo sapiens)
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PHAROS  P42285
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  • Reference Sequence
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  • Entity ID: 14
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')N16synthetic construct
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    Entity ID: 15
    MoleculeChainsLengthOrganismImage
    DNA/RNA (62-MER)O62synthetic construct
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ANP
    Query on ANP

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    M
    PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
    C10 H17 N6 O12 P3
    PVKSNHVPLWYQGJ-KQYNXXCUSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    K
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    K
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.45 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118080
    Howard Hughes Medical Institute (HHMI)United States--

    Revision History 

    • Version 1.0: 2018-06-20
      Type: Initial release
    • Version 1.1: 2018-06-27
      Changes: Data collection, Database references
    • Version 1.2: 2019-11-20
      Changes: Author supporting evidence