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 1.3 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: https://doi.org/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, 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP45473Homo 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)
Explore Q9NPD3 
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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Find proteins for Q9NQT4 (Homo sapiens)
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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 RRP42293Homo sapiensMutation(s): 0 
Gene Names: EXOSC7KIAA0116RRP42
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Find proteins for Q15024 (Homo sapiens)
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PHAROS:  Q15024
GTEx:  ENSG00000075914 
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UniProt GroupQ15024
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component MTR3272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6MTR3
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Find proteins for Q5RKV6 (Homo sapiens)
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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 RRP40277Homo sapiensMutation(s): 1 
Gene Names: EXOSC3RRP40CGI-102
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Find proteins for Q9NQT5 (Homo sapiens)
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PHAROS:  Q9NQT5
GTEx:  ENSG00000107371 
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UniProt GroupQ9NQT5
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP4296Homo sapiensMutation(s): 0 
Gene Names: EXOSC2RRP4
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Find proteins for Q13868 (Homo sapiens)
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PHAROS:  Q13868
GTEx:  ENSG00000130713 
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UniProt GroupQ13868
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component CSL4197Homo sapiensMutation(s): 0 
Gene Names: EXOSC1CSL4CGI-108
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Find proteins for Q9Y3B2 (Homo sapiens)
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PHAROS:  Q9Y3B2
GTEx:  ENSG00000171311 
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UniProt GroupQ9Y3B2
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome component 10761Homo sapiensMutation(s): 1 
Gene Names: EXOSC10PMSCLPMSCL2RRP6
EC: 3.1.13
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GTEx:  ENSG00000171824 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP44960Homo sapiensMutation(s): 4 
Gene Names: DIS3KIAA1008RRP44
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
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Find proteins for Q9Y2L1 (Homo sapiens)
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PHAROS:  Q9Y2L1
GTEx:  ENSG00000083520 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
M-phase phosphoprotein 6162Homo 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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UniProt GroupQ99547
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome RNA helicase MTR41,045Homo sapiensMutation(s): 0 
Gene Names: MTREXDOB1KIAA0052MTR4SKIV2L2
EC: 3.6.4.13
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Find proteins for P42285 (Homo sapiens)
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PHAROS:  P42285
GTEx:  ENSG00000039123 
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UniProt GroupP42285
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Entity ID: 14
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')16synthetic construct
Sequence Annotations
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA/RNA (62-MER)62synthetic construct
Sequence Annotations
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13-2998
RECONSTRUCTIONRELION2.1b1

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  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references