5xeg - Revision history

OCA at 08:00, 22 November 2023

OCA — Wed, 22 Nov 2023 08:00:47 GMT

←Older revision		Revision as of 08:00, 22 November 2023
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	==The structure of OsALKBH1==		==The structure of OsALKBH1==
-	<StructureSection load='5xeg' size='340' side='right' caption='[[5xeg]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5xeg' size='340' side='right'caption='[[5xeg]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xeg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Japanese_rice Japanese rice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xeg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XEG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=AKG:2~~-~~OXOGLUTARIC+ACID'>AKG</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~LOC_Os03g60190, OsJ_13105 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=39947 Japanese rice]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=5xeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xeg OCA], [~~http~~://pdbe.org/5xeg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xeg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xeg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xeg 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=5xeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xeg OCA], [https://pdbe.org/5xeg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xeg RCSB], [https://www.ebi.ac.uk/pdbsum/5xeg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xeg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q10BI6_ORYSJ Q10BI6_ORYSJ]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Japanese rice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Guo, Y~~]]	+	[[Category: Oryza sativa Japonica Group]]
-	[[Category: ~~Wang, C~~]]	+	[[Category: Guo Y]]
-	[[Category: ~~Zeng, Z~~]]	+	[[Category: Wang C]]
-	[[Category: ~~Oxidoreductase~~]]	+	[[Category: Zeng Z]]

OCA at 08:44, 19 December 2018

OCA — Wed, 19 Dec 2018 08:44:37 GMT

←Older revision		Revision as of 08:44, 19 December 2018
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	<StructureSection load='5xeg' size='340' side='right' caption='[[5xeg]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5xeg' size='340' side='right' caption='[[5xeg]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xeg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xeg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LOC_Os03g60190, OsJ_13105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=5xeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xeg OCA], [http://pdbe.org/5xeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xeg RCSB], [http://www.ebi.ac.uk/pdbsum/5xeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xeg 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=5xeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xeg OCA], [http://pdbe.org/5xeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xeg RCSB], [http://www.ebi.ac.uk/pdbsum/5xeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xeg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA N(6)-methyladenine (6mA) is a non-canonical DNA modification that is present at low levels in different eukaryotes(1-8), but its prevalence and genomic function in higher plants are unclear. Using mass spectrometry, immunoprecipitation and validation with analysis of single-molecule real-time sequencing, we observed that about 0.2% of all adenines are 6mA methylated in the rice genome. 6mA occurs most frequently at GAGG motifs and is mapped to about 20% of genes and 14% of transposable elements. In promoters, 6mA marks silent genes, but in bodies correlates with gene activity. 6mA overlaps with 5-methylcytosine (5mC) at CG sites in gene bodies and is complementary to 5mC at CHH sites in transposable elements. We show that OsALKBH1 may be potentially involved in 6mA demethylation in rice. The results suggest that 6mA is complementary to 5mC as an epigenomic mark in rice and reinforce a distinct role for 6mA as a gene expression-associated epigenomic mark in eukaryotes.
		+
		+	Identification and analysis of adenine N(6)-methylation sites in the rice genome.,Zhou C, Wang C, Liu H, Zhou Q, Liu Q, Guo Y, Peng T, Song J, Zhang J, Chen L, Zhao Y, Zeng Z, Zhou DX Nat Plants. 2018 Aug;4(8):554-563. doi: 10.1038/s41477-018-0214-x. Epub 2018 Jul , 30. PMID:30061746<ref>PMID:30061746</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xeg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Japanese rice]]
	[[Category: Guo, Y]]		[[Category: Guo, Y]]
	[[Category: Wang, C]]		[[Category: Wang, C]]
	[[Category: Zeng, Z]]		[[Category: Zeng, Z]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:34, 14 June 2018

OCA — Thu, 14 Jun 2018 07:34:22 GMT

←Older revision		Revision as of 07:34, 14 June 2018
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-	'''Unreleased structure'''

-	The ~~entry~~ 5xeg is ~~ON HOLD until Jul 10 2019~~	+	==The structure of OsALKBH1==
-		+	<StructureSection load='5xeg' size='340' side='right' caption='[[5xeg]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Wang~~, C., ~~Guo~~, Y., ~~Zeng~~, Z.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xeg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEG FirstGlance]. <br>
-	~~Description~~: ~~The structure of OsALKBH1~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5xeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xeg OCA], [http://pdbe.org/5xeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xeg RCSB], [http://www.ebi.ac.uk/pdbsum/5xeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xeg ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Guo, Y]]
		+	[[Category: Wang, C]]
	[[Category: Zeng, Z]]		[[Category: Zeng, Z]]
-	[[Category: ~~Wang, C]]~~	+	[[Category: Oxidoreductase]]
-	~~[[Category: Guo, Y~~]]	+

OCA at 04:01, 6 June 2018

OCA — Wed, 06 Jun 2018 04:01:39 GMT

←Older revision		Revision as of 04:01, 6 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xeg is ON HOLD until ~~Jun 05~~ 2019	+	The entry 5xeg is ON HOLD until Jul 10 2019

	Authors: Wang, C., Guo, Y., Zeng, Z.		Authors: Wang, C., Guo, Y., Zeng, Z.
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	Description: The structure of OsALKBH1		Description: The structure of OsALKBH1
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Zeng, Z]]
	[[Category: Wang, C]]		[[Category: Wang, C]]
	[[Category: Guo, Y]]		[[Category: Guo, Y]]
-	[[Category: Zeng, Z]]

OCA at 12:13, 11 April 2018

OCA — Wed, 11 Apr 2018 12:13:51 GMT

←Older revision		Revision as of 12:13, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xeg is ON HOLD until ~~Paper Publication~~	+	The entry 5xeg is ON HOLD until Jun 05 2019

	Authors: Wang, C., Guo, Y., Zeng, Z.		Authors: Wang, C., Guo, Y., Zeng, Z.
Line 7:		Line 7:
	Description: The structure of OsALKBH1		Description: The structure of OsALKBH1
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Guo, Y]]
	[[Category: Wang, C]]		[[Category: Wang, C]]
		+	[[Category: Guo, Y]]
	[[Category: Zeng, Z]]		[[Category: Zeng, Z]]

OCA at 12:05, 19 April 2017

OCA — Wed, 19 Apr 2017 12:05:44 GMT

←Older revision		Revision as of 12:05, 19 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xeg is ON HOLD	+	The entry 5xeg is ON HOLD until Paper Publication

-	Authors: ~~Changshi~~ Wang, ~~Yan~~ Guo, ~~Zhixiong~~ Zeng	+	Authors: Wang, C., Guo, Y., Zeng, Z.

	Description: The structure of OsALKBH1		Description: The structure of OsALKBH1
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Changshi Wang, Yan~~ Guo, ~~Zhixiong~~ Zeng]]	+	[[Category: Guo, Y]]
		+	[[Category: Wang, C]]
		+	[[Category: Zeng, Z]]

OCA: Protected "5xeg" [edit=sysop:move=sysop]

OCA — Wed, 12 Apr 2017 10:41:28 GMT

Protected "5xeg" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:41, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xeg is ON HOLD Authors: Changshi Wang, Yan Guo, Zhixiong Zeng Description: The structure of OsALKBH1 Category: Unreleased Structures [[Categor...

OCA — Wed, 12 Apr 2017 10:41:27 GMT

New page: '''Unreleased structure''' The entry 5xeg is ON HOLD Authors: Changshi Wang, Yan Guo, Zhixiong Zeng Description: The structure of OsALKBH1 Category: Unreleased Structures [[Categor...

New page

'''Unreleased structure'''

The entry 5xeg is ON HOLD

Authors: Changshi Wang, Yan Guo, Zhixiong Zeng

Description: The structure of OsALKBH1
[[Category: Unreleased Structures]]
[[Category: Changshi Wang, Yan Guo, Zhixiong Zeng]]