9m5x: Difference between revisions

Latest revision as of 06:20, 20 August 2025

Cryo-EM structure of Arabidopsis thaliana MET1

Structural highlights

9m5x is a 1 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:	Electron Microscopy, Resolution 3.21Å
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNMT1_ARATH Maintains chromatin CpG methylation that plays a role in genomic imprinting, regulation of embryogenesis and seed viability. Required for proper patterns of CG DNA methylation in dividing cells. Required for MEA promoter methylation in seeds.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

References

↑ Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 2002 Dec 2;21(23):6549-59. PMID:12456661 doi:10.1093/emboj/cdf657
↑ Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics. 2003 Mar;163(3):1109-22. PMID:12663548 doi:10.1093/genetics/163.3.1109
↑ Saze H, Mittelsten Scheid O, Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet. 2003 May;34(1):65-9. PMID:12669067 doi:10.1038/ng1138
↑ Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell. 2003 Dec;5(6):891-901. PMID:14667411 doi:10.1016/s1534-5807(03)00361-7
↑ Xiao W, Custard KD, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL. DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell. 2006 Apr;18(4):805-14. PMID:16531498 doi:10.1105/tpc.105.038836
↑ Xiao W, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL. Regulation of seed size by hypomethylation of maternal and paternal genomes. Plant Physiol. 2006 Nov;142(3):1160-8. PMID:17012404 doi:10.1104/pp.106.088849
↑ Kim M, Ohr H, Lee JW, Hyun Y, Fischer RL, Choi Y. Temporal and spatial downregulation of Arabidopsis MET1 activity results in global DNA hypomethylation and developmental defects. Mol Cells. 2008 Dec 31;26(6):611-5 PMID:18820427

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OCA

[1] Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 2002 Dec 2;21(23):6549-59. PMID:12456661 doi:10.1093/emboj/cdf657

[2] Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics. 2003 Mar;163(3):1109-22. PMID:12663548 doi:10.1093/genetics/163.3.1109

[3] Saze H, Mittelsten Scheid O, Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet. 2003 May;34(1):65-9. PMID:12669067 doi:10.1038/ng1138

[4] Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell. 2003 Dec;5(6):891-901. PMID:14667411 doi:10.1016/s1534-5807(03)00361-7

[5] Xiao W, Custard KD, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL. DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell. 2006 Apr;18(4):805-14. PMID:16531498 doi:10.1105/tpc.105.038836

[6] Xiao W, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL. Regulation of seed size by hypomethylation of maternal and paternal genomes. Plant Physiol. 2006 Nov;142(3):1160-8. PMID:17012404 doi:10.1104/pp.106.088849

[7] Kim M, Ohr H, Lee JW, Hyun Y, Fischer RL, Choi Y. Temporal and spatial downregulation of Arabidopsis MET1 activity results in global DNA hypomethylation and developmental defects. Mol Cells. 2008 Dec 31;26(6):611-5 PMID:18820427

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9m5x is ON HOLD  until Paper Publication
+==Cryo-EM structure of Arabidopsis thaliana MET1==
+<StructureSection load='9m5x' size='340' side='right'caption='[[9m5x]], [[Resolution|resolution]] 3.21&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9m5x]] is a 1 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=9M5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9M5X FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.21&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=9m5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9m5x OCA], [https://pdbe.org/9m5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9m5x RCSB], [https://www.ebi.ac.uk/pdbsum/9m5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9m5x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DNMT1_ARATH DNMT1_ARATH] Maintains chromatin CpG methylation that plays a role in genomic imprinting, regulation of embryogenesis and seed viability. Required for proper patterns of CG DNA methylation in dividing cells. Required for MEA promoter methylation in seeds.<ref>PMID:12456661</ref> <ref>PMID:12663548</ref> <ref>PMID:12669067</ref> <ref>PMID:14667411</ref> <ref>PMID:16531498</ref> <ref>PMID:17012404</ref> <ref>PMID:18820427</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Arita K]]
+[[Category: Kikuchi A]]

9m5x: Difference between revisions

Latest revision as of 06:20, 20 August 2025

Cryo-EM structure of Arabidopsis thaliana MET1

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Function

References

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