5YDG

Crystal structure of the Arabidopsis thaliana chloroplast RNA editing factors 2(MORF2)

• PDB DOI: https://doi.org/10.2210/pdb5YDG/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-13 Released: 2017-12-20 
• Deposition Author(s): Wang, X., Yang, J.Y., Wang, Y.L., Gao, Y.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Crystal structure of the chloroplast RNA editing factor MORF2

Yang, J., Zhang, M., Wang, X.

(2018) Biochem Biophys Res Commun 495: 2038-2043

• PubMed: 29229384 
• DOI: https://doi.org/10.1016/j.bbrc.2017.12.044
• Primary Citation of Related Structures:  
  5YDG


• PubMed Abstract: 
  

  RNA editing is a post-transcription process that alters the genetic information on RNA molecules. In plastids and mitochondria of flowering plants, the multiple organellar RNA editing factors (MORFs) interact with the PLS-type pentatricopeptide repeat (PPR) proteins and participate in RNA editing of cytidine-to-uridine conversion. The PPR proteins recognize cytidine targets around the editing sites, and the MORF proteins modulate the RNA-binding activity of the PPR proteins. Here, we report the structure of the Arabidopsis thaliana chloroplast MORF2 at 2.4 Å resolution. The structure, adopting typical MORF-box fold as observed in mitochondrial MORF1 and chloroplast MORF9, reveals an MORF1-like dimerization mode. The difference between the two dimerization modes can be attributed to F157 (corresponding F162 in MORF1 and W160 in MORF9), which causes a 60° shift upon dimerization. This observation, together with the PPR-MORF2 model, suggests a dimer-to-monomer transition during RNA editosome formation.

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Organizational Affiliation: 

School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.33 kDa 
• Atom Count: 1,879 
• Modelled Residue Count: 230 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multiple organellar RNA editing factor 2, chloroplastic	A, B	116	Arabidopsis thaliana	Mutation(s): 0  Gene Names: MORF2, DAL1, RIP2, At2g33430
UniProt
Find proteins for O22793 (Arabidopsis thaliana) Explore O22793  Go to UniProtKB:  O22793

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.209	α = 90
b = 85.88	β = 90
c = 86.559	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Wang, X., Yang, J.Y., Wang, Y.L., Gao, Y.S.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Database references
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references