6D6R

Human nuclear exosome-MTR4 RNA complex - composite map after focused 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, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation ...

    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: EXOSC9, PMSCL1
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UniProt GroupQ06265
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP41B249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4, RRP41, SKI6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43C278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8, OIP2, RRP43
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46D237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5, CML28, RRP46
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42E293Homo sapiensMutation(s): 0 
Gene Names: EXOSC7, KIAA0116, RRP42
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3F272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6, MTR3
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40G277Homo sapiensMutation(s): 1 
Gene Names: EXOSC3, RRP40, CGI-102
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4H296Homo sapiensMutation(s): 0 
Gene Names: EXOSC2, RRP4
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4I197Homo sapiensMutation(s): 0 
Gene Names: EXOSC1, CSL4, CGI-108
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome component 10J761Homo sapiensMutation(s): 1 
Gene Names: EXOSC10, PMSCL, PMSCL2, RRP6
EC: 3.1.13
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP44K960Homo sapiensMutation(s): 4 
Gene Names: DIS3, KIAA1008, RRP44
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
M-phase phosphoprotein 6L162Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH6, MPP6
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome RNA helicase MTR4M1,045Homo sapiensMutation(s): 0 
Gene Names: MTREX, DOB1, KIAA0052, MTR4, SKIV2L2
EC: 3.6.4.13
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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
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
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R [auth M]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
P [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
Q [auth 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

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View more in-depth experimental data
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