6F4A

Yeast mitochondrial RNA degradosome complex mtEXO

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.298 

wwPDB Validation   3D Report Full Report


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Literature

Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components.

Razew, M., Warkocki, Z., Taube, M., Kolondra, A., Czarnocki-Cieciura, M., Nowak, E., Labedzka-Dmoch, K., Kawinska, A., Piatkowski, J., Golik, P., Kozak, M., Dziembowski, A., Nowotny, M.

(2018) Nat Commun 9: 97-97

  • DOI: https://doi.org/10.1038/s41467-017-02570-5
  • Primary Citation of Related Structures:  
    6F3H, 6F4A

  • PubMed Abstract: 

    • Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination ...

    Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast. Here, we present the structure of mtEXO and a description of its mechanism of action. The crystal structure of Dss1 reveals domains that are responsible for interactions with Suv3. Importantly, these interactions are compatible with the conformational changes of Suv3 domains during the helicase cycle. We demonstrate that mtEXO is an intimate complex which forms an RNA-binding channel spanning its entire structure, with Suv3 helicase feeding the 3' end of the RNA toward the active site of Dss1.

    Organizational Affiliation: 

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland. mnowotny@iimcb.gov.pl.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exoribonuclease II, mitochondrialA832Nakaseomyces glabratusMutation(s): 0 
Gene Names: AO440_004157
UniProt
Find proteins for Q6FJE0 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Explore Q6FJE0 
Go to UniProtKB:  Q6FJE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6FJE0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Suv3 helicaseB644Nakaseomyces glabratusMutation(s): 0 
Gene Names: SUV3, CAGL0L12386g
EC: 3.6.4.13
UniProt
Find proteins for Q6FKD7 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Explore Q6FKD7 
Go to UniProtKB:  Q6FKD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6FKD7
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')C6Escherichia coli
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.298 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.55α = 90
b = 151.24β = 90
c = 284.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Centre PolandPoland00463

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release