Structural and biochemical characterization of the yeast exosome component Rrp40
Open accessAbstract
The exosome is a protein complex that is important in both degradation and 3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The structure comprises an S1 domain and an unusual KH (K homology) domain. Close packing of the S1 and KH domains is stabilized by a GxNG sequence, which is uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have very low intrinsic affinity for RNA. The affinity of an archaeal core exosome for RNA is significantly increased in the presence of the S1-KH subunit Rrp4, indicating that multiple subunits might contribute to cooperative binding of RNA substrates by the exosome.
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EXOSC3 encodes a core structural component of the RNA exosome complex and contains an RNA binding S1 domain, although weak RNA binding is displayed in vitro outside of the context of the full complex.
“EXOSC3 encodes a core structural component of the RNA exosome complex and contains an RNA binding S1 domain, although weak RNA binding is displayed in vitro outside of the context of the full complex38.”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [38]
The Structural overview section identifies yeast Rrp40 as an exosome subunit with an S1 domain, and the RNA-binding properties section reports little or no detectable RNA binding by isolated Rrp40 in vitro. The paper does not identify EXOSC3 or test its protein product directly; its full-complex binding experiment uses archaeal Rrp4 rather than Rrp40. (LLM, conf=0.85)
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References 31 · Cited by 62
- Authors
- Oddone, A., Lorentzen, E., Basquin, J., Gasch, A., Rybin, V., Conti, E., & Sattler, M.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Max Planck Society (DE)
- Corresponding author
- Conti, Elena
- Sattler, Michael
- Venue
- The EMBO Reports
- Published
- 2006-12-08
- Volume
- 8
- Issue
- 1
- Pages
- 63-69
- ISSN
- 1469-221X (ISSN-L)
- 1469-3178
- PMC
- PMC1796750
- OpenAlex
- W1974420185
- Cited by
- 62
- References
- 31
- Citations by year
- 2026: 2 · 2025: 4 · 2023: 2 · 2022: 4 · 2021: 4 · 2020: 1 · 2019: 5 · 2017: 3 · 2016: 1 · 2015: 3 · 2013: 5 · 2012: 3
- FWCI
- 2.04
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- EMBO Reports (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DORA PSI (Paul Scherrer Institute) (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Site cant be reached (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft
- Carlsbergfondet
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- exosomes, Saccharomyces cerevisiae, crystal structure, S1 domain, KH domain, manganese binding site, RNA binding affinity, RNA degradation, RNA-protein interactions
- MeSH terms
- Amino Acid Sequence, Exoribonucleases, Manganese, Molecular Sequence Data, RNA, Sequence Alignment, RNA-Binding Proteins, Sequence Deletion, Protein Structure, Tertiary, Crystallography, X-Ray, Nuclear Magnetic Resonance, Biomolecular, Amino Acid Motifs, Protein Subunits, Saccharomyces cerevisiae Proteins, Exosome Multienzyme Ribonuclease Complex
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