5MPY

Crystal structure of Arabidopsis thaliana RNA editing factor MORF9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.247 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of the Arabidopsis thaliana organellar RNA editing factors MORF1 and MORF9.

Haag, S.Schindler, M.Berndt, L.Brennicke, A.Takenaka, M.Weber, G.

(2017) Nucleic Acids Res. 45: 4915-4928

  • DOI: 10.1093/nar/gkx099
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In flowering plant plastids and mitochondria, multiple organellar RNA editing factor (MORF/RIP) proteins are required at most sites for efficient C to U RNA editing catalyzed by the RNA editosome. MORF proteins harbor a conserved stretch of residues ...

    In flowering plant plastids and mitochondria, multiple organellar RNA editing factor (MORF/RIP) proteins are required at most sites for efficient C to U RNA editing catalyzed by the RNA editosome. MORF proteins harbor a conserved stretch of residues (MORF-box), form homo- and heteromers and interact with selected PPR (pentatricopeptide repeat) proteins, which recognize each editing site. The molecular function of the MORF-box remains elusive since it shares no sequence similarity with known domains. We determined structures of the A. thaliana mitochondrial MORF1 and chloroplast MORF9 MORF-boxes which both adopt a novel globular fold (MORF domain). Our structures state a paradigmatic model for MORF domains and their specific dimerization via a hydrophobic interface. We cross-validate the interface by yeast two-hybrid studies and pulldown assays employing structure-based mutants. We find a structural similarity of the MORF domain to an N-terminal ferredoxin-like domain (NFLD), which confers RNA substrate positioning in bacterial 4-thio-uracil tRNA synthetases, implying direct RNA contacts of MORF proteins during RNA editing. With the MORF1 and MORF9 structures we elucidate a yet unknown fold, corroborate MORF interaction studies, validate the mechanism of MORF multimerization by structure-based mutants and pave the way towards a complete structural characterization of the plant RNA editosome.


    Organizational Affiliation

    Molekulare Botanik, Universit├Ąt Ulm, 89069 Ulm, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multiple organellar RNA editing factor 9, chloroplastic
A, B
101Arabidopsis thalianaMutation(s): 0 
Gene Names: MORF9 (RIP9)
Find proteins for Q9LPZ1 (Arabidopsis thaliana)
Go to UniProtKB:  Q9LPZ1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.247 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 73.875α = 90.00
b = 73.875β = 90.00
c = 264.938γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references