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Structure paper

TitleHelicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Journal, issue, pagesCell, Vol. 173, Issue 7, Page 1663-1677.e21, Year 2018
Publish dateJun 14, 2018
AuthorsEva-Maria Weick / M Rhyan Puno / Kurt Januszyk / John C Zinder / Michael A DiMattia / Christopher D Lima /
PubMed AbstractThe 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- ...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.
External linksCell / PubMed:29906447 / PubMed Central
MethodsEM (single particle)
Resolution3.31 - 8.22 Å
Structure data

7808

6d6q

EMDB-7808, PDB-6d6q:
Human nuclear exosome-MTR4 RNA complex - overall reconstruction
Method: EM (single particle) / Resolution: 3.45 Å

7809

6d6r

EMDB-7809, PDB-6d6r:
Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction
Method: EM (single particle) / Resolution: 3.45 Å

EMDB-7810:
Human nuclear exosome-MTR4 RNA complex - focused reconstruction on the nine-subunit core, MPP6, and EXOSC10
Method: EM (single particle) / Resolution: 3.31 Å

EMDB-7812:
Human nuclear exosome-MTR4 RNA complex - focused reconstruction on the DIS-PIN domain
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-7813:
Human nuclear exosome-MTR4 RNA complex - focused reconstruction on MTR4
Method: EM (single particle) / Resolution: 3.54 Å

EMDB-7814:
Human nuclear exosome-MTR4 RNA complex - focused reconstruction on the DIS3-RNBCS domains
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-7815:
Human nuclear exosome-MTR4 RNA complex - focused reconstruction on MTR4-dsDNA/RNA class
Method: EM (single particle) / Resolution: 3.91 Å

EMDB-7818:
Human nuclear exosome-MTR4 RNA complex - overall reconstruction - small class KOW domain open
Method: EM (single particle) / Resolution: 7.75 Å

EMDB-7819:
Human nuclear exosome-MTR4 RNA complex - overall reconstruction - small class KOW domain closed
Method: EM (single particle) / Resolution: 8.22 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsHYDROLASE / RNA exosome / RNA degradation / ribonuclease / helicase / SF2 / RNA-protein complex / translocase / nuclear

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