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Title4D structural biology-quantitative dynamics in the eukaryotic RNA exosome complex.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 7896, Year 2025
Publish dateAug 24, 2025
AuthorsJobst Liebau / Daniela Lazzaretti / Torben Fürtges / Anna Bichler / Michael Pilsl / Till Rudack / Remco Sprangers /
PubMed AbstractMolecular machines play pivotal roles in all biological processes. Most structural methods, however, are unable to directly probe molecular motions. Here, we demonstrate that dedicated NMR ...Molecular machines play pivotal roles in all biological processes. Most structural methods, however, are unable to directly probe molecular motions. Here, we demonstrate that dedicated NMR experiments can provide quantitative insights into functionally important dynamic regions in very large asymmetric protein complexes. We establish this for the 410 kDa eukaryotic RNA exosome complex that contains ten distinct protein chains. Methyl-group and fluorine NMR experiments reveal site-specific interactions among subunits and with an RNA substrate. Furthermore, we extract quantitative insights into conformational changes within the complex in response to substrate and subunit binding for regions that are invisible in static cryo-EM and crystal structures. In particular, we identify a flexible plug region that can block an aberrant route for RNA towards the active site. Based on molecular dynamics simulations and NMR data, we provide a model that shows how the flexible plug is structured in the open and closed conformations. Our work thus demonstrates that a combination of state-of-the-art structural biology methods can provide quantitative insights into large molecular machines that go significantly beyond the well-resolved and static images of biomolecular complexes, thereby adding the time domain to structural biology.
External linksNat Commun / PubMed:40849410 / PubMed Central
MethodsEM (single particle)
Resolution3.19 Å
Structure data

18825

8r1o

EMDB-18825, PDB-8r1o:
Structure of C. thermophilum RNA exosome core
Method: EM (single particle) / Resolution: 3.19 Å

Source
  • thermochaetoides thermophila dsm 1495 (fungus)
KeywordsRNA BINDING PROTEIN / nuclease / RNA degradation / RNA metabolism / RNA binding

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