4DNI

Structure of Editosome protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Explorations of linked editosome domains leading to the discovery of motifs defining conserved pockets in editosome OB-folds.

Park, Y.J.Hol, W.G.

(2012) J Struct Biol 180: 362-373

  • DOI: 10.1016/j.jsb.2012.07.012
  • Primary Citation of Related Structures:  
    4DNI

  • PubMed Abstract: 
  • Trypanosomatids form a group of protozoa which contain parasites of human, animals and plants. Several of these species cause major human diseases, including Trypanosoma brucei which is the causative agent of human African trypanosomiasis, also called sl ...

    Trypanosomatids form a group of protozoa which contain parasites of human, animals and plants. Several of these species cause major human diseases, including Trypanosoma brucei which is the causative agent of human African trypanosomiasis, also called sleeping sickness. These organisms have many highly unusual features including a unique U-insertion/deletion RNA editing process in the single mitochondrion. A key multi-protein complex, called the ∼20S editosome, or editosome, carries out a cascade of essential RNA-modifying reactions and contains a core of 12 different proteins of which six are the interaction proteins A1 to A6. Each of these interaction proteins comprises a C-terminal OB-fold and the smallest interaction protein A6 has been shown to interact with four other editosome OB-folds. Here we report the results of a "linked OB-fold" approach to obtain a view of how multiple OB-folds might interact in the core of the editosome. Constructs with variants of linked domains in 25 expression and co-expression experiments resulted in 13 soluble multi-OB-fold complexes. In several instances, these complexes were more homogeneous in size than those obtained from corresponding unlinked OB-folds. The crystal structure of A3(OB) linked to A6 could be elucidated and confirmed the tight interaction between these two OB domains as seen also in our recent complex of A3(OB) and A6 with nanobodies. In the current crystal structure of A3(OB) linked to A6, hydrophobic side chains reside in well-defined pockets of neighboring OB-fold domains. When analyzing the available crystal structures of editosome OB-folds, it appears that in five instances "Pocket 1" of A1(OB), A3(OB) and A6 is occupied by a hydrophobic side chain from a neighboring protein. In these three different OB-folds, Pocket 1 is formed by two conserved sequence motifs and an invariant arginine. These pockets might play a key role in the assembly or mechanism of the editosome by interacting with hydrophobic side chains from other proteins.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion protein of RNA-editing complex proteins MP42 and MP18 A257Trypanosoma bruceiTrypanosoma brucei brucei TREU927
This entity is chimeric
Mutation(s): 0 
Gene Names: KREPA3KREPA6
Find proteins for Q38B90 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38B90 
Go to UniProtKB:  Q38B90
Find proteins for Q95W13 (Trypanosoma brucei)
Explore Q95W13 
Go to UniProtKB:  Q95W13
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.733α = 90
b = 59.418β = 90
c = 100.755γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-02-08 
  • Released Date: 2012-12-26 
  • Deposition Author(s): Park, Y.-J., Hol, W.

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2017-11-15
    Changes: Refinement description