5v21 - Revision history

OCA at 13:39, 4 October 2023

2023-10-04T13:39:49Z

← Older revision		Revision as of 13:39, 4 October 2023
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	<StructureSection load='5v21' size='340' side='right'caption='[[5v21]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='5v21' size='340' side='right'caption='[[5v21]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v21]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V21 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V21 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v21]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V21 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <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]] 2.415Å</td></tr>
	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5v22\|5v22~~]]</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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"~~>SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</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=5v21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v21 OCA], [https://pdbe.org/5v21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v21 RCSB], [https://www.ebi.ac.uk/pdbsum/5v21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v21 ProSAT]</span></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43]~~ </~~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=5v21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v21 OCA], [~~http~~://pdbe.org/5v21 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v21 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v21 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v21 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/SETD2_HUMAN SETD2_HUMAN]] Histone methyltransferase that methylates 'Lys-36' of histone H3. H3 'Lys-36' methylation represents a specific tag for epigenetic transcriptional activation. Probably plays a role in chromatin structure modulation during elongation via its interaction with hyperphosphorylated POLR2A. Binds DNA at promoters. May also act as a transcription activator that binds to promoters. Binds to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.<ref>PMID:16118227</ref>		[https://www.uniprot.org/uniprot/SETD2_HUMAN SETD2_HUMAN] Histone methyltransferase that methylates 'Lys-36' of histone H3. H3 'Lys-36' methylation represents a specific tag for epigenetic transcriptional activation. Probably plays a role in chromatin structure modulation during elongation via its interaction with hyperphosphorylated POLR2A. Binds DNA at promoters. May also act as a transcription activator that binds to promoters. Binds to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.<ref>PMID:16118227</ref>
	<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: ~~Histone-lysine N-methyltransferase]]~~		[[Category: Homo sapiens]]
	~~[[Category: Human~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Tong, L]]		[[Category: Tong L]]
	[[Category: Zhang, Y]]		[[Category: Zhang Y]]
	~~[[Category: Methyltransferase]]~~
	~~[[Category: Transferase~~]]

OCA at 09:26, 1 January 2020

2020-01-01T09:26:41Z

← Older revision		Revision as of 09:26, 1 January 2020
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	==Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM==		==Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM==
	<StructureSection load='5v21' size='340' side='right' caption='[[5v21]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='5v21' size='340' side='right'caption='[[5v21]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v21]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V21 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v21]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V21 FirstGlance]. <br>
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	==See Also==		==See Also==
	*[[Histone methyltransferase\|Histone methyltransferase]]		*[[Histone methyltransferase 3D structures\|Histone methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Histone-lysine N-methyltransferase]]		[[Category: Histone-lysine N-methyltransferase]]
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Tong, L]]		[[Category: Tong, L]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:13, 8 March 2018

2018-03-08T06:13:02Z

← Older revision		Revision as of 06:13, 8 March 2018
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	</div>		</div>
	<div class="pdbe-citations 5v21" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v21" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Histone methyltransferase\|Histone methyltransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:38, 6 November 2017

2017-11-06T14:38:41Z

← Older revision		Revision as of 14:38, 6 November 2017
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	<StructureSection load='5v21' size='340' side='right' caption='[[5v21]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='5v21' size='340' side='right' caption='[[5v21]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v21]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V21 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v21]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V21 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v22\|5v22]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v22\|5v22]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=5v21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v21 OCA], [http://pdbe.org/5v21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v21 RCSB], [http://www.ebi.ac.uk/pdbsum/5v21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v21 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=5v21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v21 OCA], [http://pdbe.org/5v21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v21 RCSB], [http://www.ebi.ac.uk/pdbsum/5v21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v21 ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Histone-lysine N-methyltransferase]]		[[Category: Histone-lysine N-methyltransferase]]
			[[Category: Human]]
	[[Category: Tong, L]]		[[Category: Tong, L]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:07, 29 March 2017

2017-03-29T07:07:01Z

← Older revision		Revision as of 07:07, 29 March 2017
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SETD2_HUMAN SETD2_HUMAN]] Histone methyltransferase that methylates 'Lys-36' of histone H3. H3 'Lys-36' methylation represents a specific tag for epigenetic transcriptional activation. Probably plays a role in chromatin structure modulation during elongation via its interaction with hyperphosphorylated POLR2A. Binds DNA at promoters. May also act as a transcription activator that binds to promoters. Binds to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.<ref>PMID:16118227</ref>		[[http://www.uniprot.org/uniprot/SETD2_HUMAN SETD2_HUMAN]] Histone methyltransferase that methylates 'Lys-36' of histone H3. H3 'Lys-36' methylation represents a specific tag for epigenetic transcriptional activation. Probably plays a role in chromatin structure modulation during elongation via its interaction with hyperphosphorylated POLR2A. Binds DNA at promoters. May also act as a transcription activator that binds to promoters. Binds to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.<ref>PMID:16118227</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Histone H3 lysine 36 methylation (H3K36me) is critical for epigenetic regulation and mutations at or near H3K36 are associated with distinct types of cancers. H3K36M dominantly inhibits H3K36me on wild-type histones, whereas H3G34R/V selectively affects H3K36me on the same histone tail. Here we report the crystal structures of SETD2 SET domain in complex with an H3K36M peptide and SAM or SAH. There are large conformational changes in the substrate binding regions of the SET domain, and the K36M residue interacts with the catalytic pocket of SETD2. H3G34 is surrounded by a very narrow tunnel, which excludes larger amino acid side chains. H3P38 is in the trans configuration, and the cis configuration is incompatible with SETD2 binding. Finally, mutations of H3G34 or H3P38 alleviate the inhibitory effects of H3K36M on H3K36me, demonstrating that the stable interaction of H3K36M with SETD2 is critical for its inhibitory effects.

			Molecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation.,Zhang Y, Shan CM, Wang J, Bao K, Tong L, Jia S Sci Rep. 2017 Mar 3;7:43906. doi: 10.1038/srep43906. PMID:28256625<ref>PMID:28256625</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5v21" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:48, 22 March 2017

2017-03-22T16:48:27Z

← Older revision		Revision as of 16:48, 22 March 2017
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5v21 is ~~ON HOLD~~		==Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM==
			<StructureSection load='5v21' size='340' side='right' caption='[[5v21]], [[Resolution\|resolution]] 2.42Å' scene=''>
	~~Authors~~: ~~Zhang~~, Y., ~~Tong~~, L.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5v21]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V21 FirstGlance]. <br>
	~~Description~~: ~~Crystal structure~~ of ~~SETD2 SET~~-~~domain~~ with ~~H3K36M peptide and SAM~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v22\|5v22]]</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </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=5v21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v21 OCA], [http://pdbe.org/5v21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v21 RCSB], [http://www.ebi.ac.uk/pdbsum/5v21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v21 ProSAT]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/SETD2_HUMAN SETD2_HUMAN]] Histone methyltransferase that methylates 'Lys-36' of histone H3. H3 'Lys-36' methylation represents a specific tag for epigenetic transcriptional activation. Probably plays a role in chromatin structure modulation during elongation via its interaction with hyperphosphorylated POLR2A. Binds DNA at promoters. May also act as a transcription activator that binds to promoters. Binds to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.<ref>PMID:16118227</ref>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Histone-lysine N-methyltransferase]]
	[[Category: Tong, L]]		[[Category: Tong, L]]
	[[Category: Zhang, Y]]		[[Category: Zhang, Y]]
			[[Category: Methyltransferase]]
			[[Category: Transferase]]

OCA at 19:38, 15 March 2017

2017-03-15T19:38:03Z

← Older revision		Revision as of 19:38, 15 March 2017
Line 3:		Line 3:
	The entry 5v21 is ON HOLD		The entry 5v21 is ON HOLD

	Authors: ~~Yinglu~~ Zhang, ~~Liang~~ Tong		Authors: Zhang, Y., Tong, L.

	Description: Crystal structure of SETD2 SET-domain with H3K36M peptide and SAM		Description: Crystal structure of SETD2 SET-domain with H3K36M peptide and SAM
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: ~~Yinglu~~ Zhang, ~~Liang Tong~~]]		[[Category: Tong, L]]
			[[Category: Zhang, Y]]

OCA: Protected "5v21" [edit=sysop:move=sysop]

2017-03-09T15:15:00Z

Protected "5v21" [edit=sysop:move=sysop]

← Older revision	Revision as of 15:15, 9 March 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5v21 is ON HOLD Authors: Yinglu Zhang, Liang Tong Description: Crystal structure of SETD2 SET-domain with H3K36M peptide and SAM [[Category: Unrele...

2017-03-09T15:14:59Z

New page: '''Unreleased structure''' The entry 5v21 is ON HOLD Authors: Yinglu Zhang, Liang Tong Description: Crystal structure of SETD2 SET-domain with H3K36M peptide and SAM [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 5v21 is ON HOLD

Authors: Yinglu Zhang, Liang Tong

Description: Crystal structure of SETD2 SET-domain with H3K36M peptide and SAM
[[Category: Unreleased Structures]]
[[Category: Yinglu Zhang, Liang Tong]]