6ois is a 6 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
[RDM1_ARATH] Regulator of RNA-directed DNA methylation (RdDM). Binds to single-stranded methyl DNA. Involved in the assembly of RNA polymerase V (Pol V) transcription initiation or elongation complexes at the chromatin, as a componant of the DDR complex.[1][2][3] [DMS3_ARATH] Component of the RNA-directed DNA methylation (RdDM) machinery, probably by facilitating an RNAi-mediated epigenetic modification involving secondary siRNAs and spreading of DNA methylation, thus leading to gene silencing. Involved in the assembly of RNA polymerase V (Pol V) transcription initiation or elongation complexes at the chromatin, as a component of the DDR complex. Required for de novo DNA methylation.[4][5][6][7][8]
Publication Abstract from PubMed
Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment-DR (DMS3-RDM1) and DDR' (DMS3-RDM1-DRD1 peptide), at 3.6 A and 3.5 A resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment.
CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.,Wongpalee SP, Liu S, Gallego-Bartolome J, Leitner A, Aebersold R, Liu W, Yen L, Nohales MA, Kuo PH, Vashisht AA, Wohlschlegel JA, Feng S, Kay SA, Zhou ZH, Jacobsen SE Nat Commun. 2019 Sep 2;10(1):3916. doi: 10.1038/s41467-019-11759-9. PMID:31477705[9]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
↑ Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA, Jacobsen SE. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol. 2010 May 25;20(10):951-6. doi: 10.1016/j.cub.2010.03.062. Epub 2010, Apr 22. PMID:20409711 doi:http://dx.doi.org/10.1016/j.cub.2010.03.062
↑ Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 2010 May 6;465(7294):106-9. doi: 10.1038/nature09025. Epub 2010 Apr 21. PMID:20410883 doi:http://dx.doi.org/10.1038/nature09025
↑ Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol. 2012 Sep;19(9):870-5. doi: 10.1038/nsmb.2354. Epub 2012 Aug , 5. PMID:22864289 doi:http://dx.doi.org/10.1038/nsmb.2354
↑ Kanno T, Bucher E, Daxinger L, Huettel B, Bohmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ. A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet. 2008 May;40(5):670-5. doi: 10.1038/ng.119. Epub 2008 Apr 20. PMID:18425128 doi:http://dx.doi.org/10.1038/ng.119
↑ 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
↑ Lee TF, Gurazada SG, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC. RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics. 2012 Jul;7(7):781-95. doi: 10.4161/epi.20290. Epub 2012 Jul 1. PMID:22647529 doi:http://dx.doi.org/10.4161/epi.20290
↑ Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol. 2012 Sep;19(9):870-5. doi: 10.1038/nsmb.2354. Epub 2012 Aug , 5. PMID:22864289 doi:http://dx.doi.org/10.1038/nsmb.2354
↑ Wongpalee SP, Liu S, Gallego-Bartolome J, Leitner A, Aebersold R, Liu W, Yen L, Nohales MA, Kuo PH, Vashisht AA, Wohlschlegel JA, Feng S, Kay SA, Zhou ZH, Jacobsen SE. CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Nat Commun. 2019 Sep 2;10(1):3916. doi: 10.1038/s41467-019-11759-9. PMID:31477705 doi:http://dx.doi.org/10.1038/s41467-019-11759-9
