4DK6

Structure of Editosome protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The structure of the C-terminal domain of the largest editosome interaction protein and its role in promoting RNA binding by RNA-editing ligase L2.

Park, Y.J.Budiarto, T.Wu, M.Pardon, E.Steyaert, J.Hol, W.G.

(2012) Nucleic Acids Res. 40: 6966-6977

  • DOI: 10.1093/nar/gks369
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Trypanosomatids, such as the sleeping sickness parasite Trypanosoma brucei, contain a ∼ 20S RNA-editing complex, also called the editosome, which is required for U-insertion/deletion editing of mitochondrial mRNAs. The editosome contains a core of 12 ...

    Trypanosomatids, such as the sleeping sickness parasite Trypanosoma brucei, contain a ∼ 20S RNA-editing complex, also called the editosome, which is required for U-insertion/deletion editing of mitochondrial mRNAs. The editosome contains a core of 12 proteins including the large interaction protein A1, the small interaction protein A6, and the editing RNA ligase L2. Using biochemical and structural data, we identified distinct domains of T. brucei A1 which specifically recognize A6 and L2. We provide evidence that an N-terminal domain of A1 interacts with the C-terminal domain of L2. The C-terminal domain of A1 appears to be required for the interaction with A6 and also plays a key role in RNA binding by the RNA-editing ligase L2 in trans. Three crystal structures of the C-terminal domain of A1 have been elucidated, each in complex with a nanobody as a crystallization chaperone. These structures permitted the identification of putative dsRNA recognition sites. Mutational analysis of conserved residues of the C-terminal domain identified Arg703, Arg731 and Arg734 as key requirements for RNA binding. The data show that the editing RNA ligase activity is modulated by a novel mechanism, i.e. by the trans-acting RNA binding C-terminal domain of A1.


    Organizational Affiliation

    Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
single domain antibody VHH
A, B
133N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-editing complex protein MP81
C, D
105Trypanosoma bruceiMutation(s): 0 
Find proteins for Q95W15 (Trypanosoma brucei)
Go to UniProtKB:  Q95W15
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.026α = 90.00
b = 40.882β = 92.55
c = 61.281γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-02-03 
  • Released Date: 2012-07-04 
  • Deposition Author(s): Park, Y.-J., Hol, W.

Revision History 

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-08-22
    Type: Database references
  • Version 1.2: 2013-09-18
    Type: Source and taxonomy
  • Version 1.3: 2017-08-02
    Type: Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-15
    Type: Refinement description