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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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: 10.1038/s41467-017-02570-5
  • Primary Citation of Related Structures:  

  • 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 (mt ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exoribonuclease II, mitochondrial
A
832Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65)Mutation(s): 0 
Gene Names: DSS1
Find proteins for Q6FJE0 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Go to UniProtKB:  Q6FJE0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Suv3 helicase
B
644Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65)Mutation(s): 0 
Gene Names: SUV3
Find proteins for Q6FKD7 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Go to UniProtKB:  Q6FKD7
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')C6Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.296 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 104.550α = 90.00
b = 151.240β = 90.00
c = 284.220γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Centre PolandPoland00463

Revision History 

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