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5z8n

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Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide

Structural highlights

5z8n is a 6 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 3.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EBS_ARATH Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulating the transcription of target genes (PubMed:25281686). Negative regulator in developmental processes in a gibberellic acid- (GA-) dependent manner, such as germination, flowering induction, and flower organ specification, probably by modulating developmental gene expression (PubMed:11340178, PubMed:25281686). Involved in the chromatin-mediated repression of floral initiation and controls genes regulating flowering (PubMed:25281686). Negatively regulates the expression of the floral integrator FT epigenetically, by preventing high levels of H3 acetylation, thus maintaining an inactive chromatin conformation at FT locus (PubMed:25281686, PubMed:12837946).^[1] ^[2] ^[3]

Publication Abstract from PubMed

The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes(1-5). In plants, timely transition to a flowering state is crucial for successful reproduction(6-9). EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis thaliana(10,11). We found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. We observed co-enrichment of a subset of EBS-associated genes with H3K4me3, H3K27me3, and Polycomb repressor complex 2 (PRC2). Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3. This binding balance was critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induced early floral transition. Our results identify a bivalent chromatin reader capable of recognizing two antagonistic histone marks, and we propose a distinct mechanism of interaction between active and repressive chromatin states.

EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.,Yang Z, Qian S, Scheid RN, Lu L, Chen X, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J, Zhong X Nat Genet. 2018 Sep;50(9):1247-1253. doi: 10.1038/s41588-018-0187-8. Epub 2018, Aug 6. PMID:30082787^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gomez-Mena C, Pineiro M, Franco-Zorrilla JM, Salinas J, Coupland G, Martinez-Zapater JM. early bolting in short days: an Arabidopsis mutation that causes early flowering and partially suppresses the floral phenotype of leafy. Plant Cell. 2001 May;13(5):1011-24. PMID:11340178
↑ Pineiro M, Gomez-Mena C, Schaffer R, Martinez-Zapater JM, Coupland G. EARLY BOLTING IN SHORT DAYS is related to chromatin remodeling factors and regulates flowering in Arabidopsis by repressing FT. Plant Cell. 2003 Jul;15(7):1552-62. PMID:12837946
↑ Lopez-Gonzalez L, Mouriz A, Narro-Diego L, Bustos R, Martinez-Zapater JM, Jarillo JA, Pineiro M. Chromatin-dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins. Plant Cell. 2014 Oct;26(10):3922-38. doi: 10.1105/tpc.114.130781. Epub 2014 Oct, 3. PMID:25281686 doi:http://dx.doi.org/10.1105/tpc.114.130781
↑ Yang Z, Qian S, Scheid RN, Lu L, Chen X, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J, Zhong X. EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nat Genet. 2018 Sep;50(9):1247-1253. doi: 10.1038/s41588-018-0187-8. Epub 2018, Aug 6. PMID:30082787 doi:http://dx.doi.org/10.1038/s41588-018-0187-8

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5z8n"

Categories: Arabidopsis thaliana | Large Structures | Du J | Yang Z

@@ Line 1: / Line 1: @@
 ==Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide==
-<StructureSection load='5z8n' size='340' side='right' caption='[[5z8n]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+<StructureSection load='5z8n' size='340' side='right'caption='[[5z8n]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5z8n]] 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=5Z8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z8N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5z8n]] 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=5Z8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z8N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EBS, At4g22140, F1N20.240 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=5z8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z8n OCA], [https://pdbe.org/5z8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z8n RCSB], [https://www.ebi.ac.uk/pdbsum/5z8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z8n ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5z8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z8n OCA], [http://pdbe.org/5z8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z8n RCSB], [http://www.ebi.ac.uk/pdbsum/5z8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z8n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/EBS_ARATH EBS_ARATH]] Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulating the transcription of target genes (PubMed:25281686). Negative regulator in developmental processes in a gibberellic acid- (GA-) dependent manner, such as germination, flowering induction, and flower organ specification, probably by modulating developmental gene expression (PubMed:11340178, PubMed:25281686). Involved in the chromatin-mediated repression of floral initiation and controls genes regulating flowering (PubMed:25281686). Negatively regulates the expression of the floral integrator FT epigenetically, by preventing high levels of H3 acetylation, thus maintaining an inactive chromatin conformation at FT locus (PubMed:25281686, PubMed:12837946).<ref>PMID:11340178</ref> <ref>PMID:12837946</ref> <ref>PMID:25281686</ref>
+[https://www.uniprot.org/uniprot/EBS_ARATH EBS_ARATH] Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulating the transcription of target genes (PubMed:25281686). Negative regulator in developmental processes in a gibberellic acid- (GA-) dependent manner, such as germination, flowering induction, and flower organ specification, probably by modulating developmental gene expression (PubMed:11340178, PubMed:25281686). Involved in the chromatin-mediated repression of floral initiation and controls genes regulating flowering (PubMed:25281686). Negatively regulates the expression of the floral integrator FT epigenetically, by preventing high levels of H3 acetylation, thus maintaining an inactive chromatin conformation at FT locus (PubMed:25281686, PubMed:12837946).<ref>PMID:11340178</ref> <ref>PMID:12837946</ref> <ref>PMID:25281686</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Du, J]]
+[[Category: Large Structures]]
-[[Category: Yang, Z]]
+[[Category: Du J]]
-[[Category: Bah]]
+[[Category: Yang Z]]
-[[Category: Eb]]
-[[Category: Gene regulation]]
-[[Category: H3k4me2]]
-[[Category: Histone reader]]
-[[Category: Phd]]

5z8n

From Proteopedia

Current revision

Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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