5MPW

Crystal structure of Arabidopsis thaliana RNA editing factor MORF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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This is version 1.3 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:  
    5MPW, 5MPX, 5MPY

  • 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 (MORF-box), form homo- and heteromers and interact with selected PPR (pentatricopeptide repeat) proteins, which recognize each editing site ...

    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

    Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multiple organellar RNA editing factor 1, mitochondrialA, B, C, D115Arabidopsis thalianaMutation(s): 0 
Gene Names: MORF1RIP8At4g20020
UniProt
Find proteins for O49429 (Arabidopsis thaliana)
Explore O49429 
Go to UniProtKB:  O49429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO49429
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
HA [auth D],
N [auth A],
U [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BR
Query on BR

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
AA [auth C],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.28α = 98.1
b = 44.94β = 91.98
c = 68.2γ = 111.96
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Database references
  • Version 1.3: 2017-12-27
    Changes: Structure summary