4E8U

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

Summary for 4E8U

• Entry DOI: 10.2210/pdb4e8u/pdb
• Descriptor: Putative uncharacterized protein T8P19.180, SULFATE ION (3 entities in total)
• Functional Keywords: xs domain, rna binding protein, rna directed dna methylation, rna
• Biological source: Arabidopsis thaliana (mouse-ear cress,thale-cress)
• Total number of polymer chains: 2
• Total formula weight: 39648.48

Authors

Simanshu, D.K.,Patel, D.J. (deposition date: 2012-03-20, release date: 2012-06-06, Last modification date: 2024-02-28)

Primary citation

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.
INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.
Proc.Natl.Acad.Sci.USA, 109:8374-8381, 2012

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.

PubMed: 22592791
DOI: 10.1073/pnas.1206638109

Experimental method

X-RAY DIFFRACTION (2.701 Å)