Proteopedia

4e8u

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

Structural highlights

4e8u is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.701Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IDN2_ARATH Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway (PubMed:22570638, PubMed:22592791) and downstream of small interfering RNA (siRNA) formation (PubMed:22810086). Required for de novo DNA methylation, siRNA accumulation and siRNA-mediated maintenance methylation (PubMed:19915591). Required for several post-transcriptional gene silencing pathways (PubMed:20059743). Binds double-stranded RNAs (dsRNAs) with 5'-overhangs through its XS domain (PubMed:19915591, PubMed:20059743). Binds long non-coding RNA (lncRNA) in an AGO4-dependent manner and associates with DRM2, resulting in DNA methylation of RdDM target loci (PubMed:23246435, PubMed:24862207). Mediates the silencing of a subset of MORC6 target loci (PubMed:27171427).[1] [2] [3] [4] [5] [6] [7] [8]

References

  1. ↑ Ausin I, Mockler TC, Chory J, Jacobsen SE. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat Struct Mol Biol. 2009 Dec;16(12):1325-7. doi: 10.1038/nsmb.1690. Epub 2009, Nov 15. PMID:19915591 doi:http://dx.doi.org/10.1038/nsmb.1690
  2. ↑ Zheng Z, Xing Y, He XJ, Li W, Hu Y, Yadav SK, Oh J, Zhu JK. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. Plant J. 2010 Apr 1;62(1):92-9. doi: 10.1111/j.1365-313X.2010.04130.x. Epub 2010 , Jan 6. PMID:20059743 doi:http://dx.doi.org/10.1111/j.1365-313X.2010.04130.x
  3. ↑ Zhang CJ, Ning YQ, Zhang SW, Chen Q, Shao CR, Guo YW, Zhou JX, Li L, Chen S, He XJ. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. PLoS Genet. 2012;8(5):e1002693. doi: 10.1371/journal.pgen.1002693. Epub 2012 May , 3. PMID:22570638 doi:http://dx.doi.org/10.1371/journal.pgen.1002693
  4. ↑ Ausin I, Greenberg MV, Simanshu DK, Hale CJ, Vashisht AA, Simon SA, Lee TF, Feng S, Espanola SD, Meyers BC, Wohlschlegel JA, Patel DJ, Jacobsen SE. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8374-81. Epub 2012 May 16. PMID:22592791 doi:10.1073/pnas.1206638109
  5. ↑ Finke A, Kuhlmann M, Mette MF. IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation. Epigenetics. 2012 Aug;7(8):950-60. doi: 10.4161/epi.21237. Epub 2012 Jul 19. PMID:22810086 doi:http://dx.doi.org/10.4161/epi.21237
  6. ↑ Zhu Y, Rowley MJ, Bohmdorfer G, Wierzbicki AT. A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell. 2013 Jan 24;49(2):298-309. doi: 10.1016/j.molcel.2012.11.011. Epub 2012, Dec 13. PMID:23246435 doi:http://dx.doi.org/10.1016/j.molcel.2012.11.011
  7. ↑ Bohmdorfer G, Rowley MJ, Kucinski J, Zhu Y, Amies I, Wierzbicki AT. RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA. Plant J. 2014 Jul;79(2):181-91. doi: 10.1111/tpj.12563. Epub 2014 Jun 23. PMID:24862207 doi:http://dx.doi.org/10.1111/tpj.12563
  8. ↑ Liu ZW, Zhou JX, Huang HW, Li YQ, Shao CR, Li L, Cai T, Chen S, He XJ. Two Components of the RNA-Directed DNA Methylation Pathway Associate with MORC6 and Silence Loci Targeted by MORC6 in Arabidopsis. PLoS Genet. 2016 May 12;12(5):e1006026. doi: 10.1371/journal.pgen.1006026., eCollection 2016 May. PMID:27171427 doi:http://dx.doi.org/10.1371/journal.pgen.1006026

4e8u, resolution 2.70Å

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