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| | <SX load='6ois' size='340' side='right' viewer='molstar' caption='[[6ois]], [[Resolution|resolution]] 3.60Å' scene=''> | | <SX load='6ois' size='340' side='right' viewer='molstar' caption='[[6ois]], [[Resolution|resolution]] 3.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ois]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OIS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OIS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ois]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OIS FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RDM1, At3g22680, MWI23.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH]), DMS3, IDN1, At3g49250, F2K15.110 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.6Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ois FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ois OCA], [http://pdbe.org/6ois PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ois RCSB], [http://www.ebi.ac.uk/pdbsum/6ois PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ois ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ois FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ois OCA], [https://pdbe.org/6ois PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ois RCSB], [https://www.ebi.ac.uk/pdbsum/6ois PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ois ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RDM1_ARATH 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.<ref>PMID:20409711</ref> <ref>PMID:20410883</ref> <ref>PMID:22864289</ref> [[http://www.uniprot.org/uniprot/DMS3_ARATH 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.<ref>PMID:18425128</ref> <ref>PMID:19377477</ref> <ref>PMID:19915591</ref> <ref>PMID:22647529</ref> <ref>PMID:22864289</ref> | + | [https://www.uniprot.org/uniprot/RDM1_ARATH 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.<ref>PMID:20409711</ref> <ref>PMID:20410883</ref> <ref>PMID:22864289</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == 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.
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| - | | + | |
| - | 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<ref>PMID:31477705</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6ois" style="background-color:#fffaf0;"></div>
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Jacobsen, S E]] | + | [[Category: Jacobsen SE]] |
| - | [[Category: Liu, S]] | + | [[Category: Liu S]] |
| - | [[Category: Wongpalee, S P]] | + | [[Category: Wongpalee SP]] |
| - | [[Category: Zhou, Z H]] | + | [[Category: Zhou ZH]] |
| - | [[Category: Coiled-coil]]
| + | |
| - | [[Category: Plant protein]]
| + | |
| - | [[Category: Rna-directed dna methylation]]
| + | |
| - | [[Category: Smc-hinge]]
| + | |
| - | [[Category: Snf2]]
| + | |
| Structural highlights
Function
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]
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
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