Crystal structure of Arabidopsis IDN2 XS domain along with a small segment of adjacent coiled-coil region

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

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INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.

Ausin, I.Greenberg, M.V.Simanshu, D.K.Hale, C.J.Vashisht, A.A.Simon, S.A.Lee, T.F.Feng, S.Espanola, S.D.Meyers, B.C.Wohlschlegel, J.A.Patel, D.J.Jacobsen, S.E.

(2012) Proc Natl Acad Sci U S A 109: 8374-8381

  • DOI: https://doi.org/10.1073/pnas.1206638109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.

  • Organizational Affiliation

    Department of Molecular, Cell, and Developmental Biology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein T8P19.180A,
B [auth C]
172Arabidopsis thalianaMutation(s): 0 
Gene Names: IDN2T8P19.180
Find proteins for Q8VZ79 (Arabidopsis thaliana)
Explore Q8VZ79 
Go to UniProtKB:  Q8VZ79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VZ79
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.37α = 90
b = 207.022β = 90
c = 119.629γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations