5j9u - Revision history

OCA at 10:56, 6 September 2023

OCA — Wed, 06 Sep 2023 10:56:13 GMT

←Older revision		Revision as of 10:56, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5j9u' size='340' side='right'caption='[[5j9u]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='5j9u' size='340' side='right'caption='[[5j9u]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j9u]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J9U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J9U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j9u]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J9U FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</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]] 2.95Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j9w\|5j9w]]~~, [[~~5j9t~~\|~~5j9t]], [[5j9q\|5j9q~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ESA1, YOR244W, O5257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=559292 Baker's yeast]), EAF6, YJR082C, J1854 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), EPL1, YFL024C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), YNG2, EAF4, NBN1, YHR090C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5j9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j9u OCA], [https://pdbe.org/5j9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j9u RCSB], [https://www.ebi.ac.uk/pdbsum/5j9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j9u 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_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48]~~ </~~span~~></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=5j9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j9u OCA], [~~http~~://pdbe.org/5j9u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j9u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j9u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j9u ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/YNG2_YEAST YNG2_YEAST]] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. Involved in cell cycle progression and meiosis.<ref>PMID:10805724</ref> <ref>PMID:11544250</ref> <ref>PMID:11604499</ref> <ref>PMID:12417725</ref> [[http://www.uniprot.org/uniprot/ESA1_YEAST ESA1_YEAST]] Catalytic component of the NuA4 histone acetyltransferase (HAT) complex which is involved in epigenetic transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4, H3, H2B, H2A and H2A variant H2A.Z. Acetylates histone H4 to form H4K5ac, H4K8ac, H4K12ac and H4K16ac, histone H3 to form H3K14ac, histone H2B to form H2BK16ac, histone H2A to form H2AK4ac and H2AK7ac, and histone variant H2A.Z to form H2A.ZK14ac. Acetylation of histone H4 is essential for DNA double-strand break repair through homologous recombination. Involved in cell cycle progression. Recruitment to promoters depends on H3K4me.<ref>PMID:9858608</ref> <ref>PMID:10082517</ref> <ref>PMID:10835360</ref> <ref>PMID:10911987</ref> <ref>PMID:12353039</ref> <ref>PMID:15175650</ref> <ref>PMID:15494307</ref> <ref>PMID:15045029</ref> <ref>PMID:15923609</ref> [[http://www.uniprot.org/uniprot/EPL1_YEAST EPL1_YEAST]] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. Involved in gene silencing by neighboring heterochromatin, blockage of the silencing spreading along the chromosome, and required for cell cycle progression through G2/M.<ref>PMID:10911987</ref> <ref>PMID:12782659</ref> <ref>PMID:14966276</ref> <ref>PMID:15045029</ref> [[http://www.uniprot.org/uniprot/EAF6_YEAST EAF6_YEAST]] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. Component of the NuA3 histone acetyltransferase complex, that acetylates Lys-14 of histone H3. Recruitment of NuA3 to nucleosomes requires methylated histone H3. In conjunction with the FACT complex, NuA3 may be involved in transcriptional regulation.<ref>PMID:17157260</ref>	+	[https://www.uniprot.org/uniprot/ESA1_YEAST ESA1_YEAST] Catalytic component of the NuA4 histone acetyltransferase (HAT) complex which is involved in epigenetic transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4, H3, H2B, H2A and H2A variant H2A.Z. Acetylates histone H4 to form H4K5ac, H4K8ac, H4K12ac and H4K16ac, histone H3 to form H3K14ac, histone H2B to form H2BK16ac, histone H2A to form H2AK4ac and H2AK7ac, and histone variant H2A.Z to form H2A.ZK14ac. Acetylation of histone H4 is essential for DNA double-strand break repair through homologous recombination. Involved in cell cycle progression. Recruitment to promoters depends on H3K4me.<ref>PMID:9858608</ref> <ref>PMID:10082517</ref> <ref>PMID:10835360</ref> <ref>PMID:10911987</ref> <ref>PMID:12353039</ref> <ref>PMID:15175650</ref> <ref>PMID:15494307</ref> <ref>PMID:15045029</ref> <ref>PMID:15923609</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
-	[[Category: Histone acetyltransferase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chen, Z C~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Xu, P~~]]	+	[[Category: Chen ZC]]
-	[[Category: ~~Acetylation]]~~	+	[[Category: Xu P]]
-	~~[[Category: Histone]]~~	+
-	~~[[Category: Nua4]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:39, 10 June 2020

OCA — Wed, 10 Jun 2020 07:39:19 GMT

←Older revision		Revision as of 07:39, 10 June 2020
Line 1:		Line 1:

	==Crystal structure of the NuA4 core complex==		==Crystal structure of the NuA4 core complex==
-	<StructureSection load='5j9u' size='340' side='right' caption='[[5j9u]], [[Resolution\|resolution]] 2.95Å' scene=''>	+	<StructureSection load='5j9u' size='340' side='right'caption='[[5j9u]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j9u]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J9U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J9U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j9u]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J9U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J9U FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j9w\|5j9w]], [[5j9t\|5j9t]], [[5j9q\|5j9q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j9w\|5j9w]], [[5j9t\|5j9t]], [[5j9q\|5j9q]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ESA1, YOR244W, O5257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), EAF6, YJR082C, J1854 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), EPL1, YFL024C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), YNG2, EAF4, NBN1, YHR090C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=5j9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j9u OCA], [http://pdbe.org/5j9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j9u RCSB], [http://www.ebi.ac.uk/pdbsum/5j9u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j9u ProSAT]</span></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=5j9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j9u OCA], [http://pdbe.org/5j9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j9u RCSB], [http://www.ebi.ac.uk/pdbsum/5j9u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j9u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5j9u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5j9u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone acetyltransferase 3D structures\|Histone acetyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Histone acetyltransferase]]		[[Category: Histone acetyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Chen, Z C]]		[[Category: Chen, Z C]]
	[[Category: Xu, P]]		[[Category: Xu, P]]

OCA at 18:32, 26 October 2016

OCA — Wed, 26 Oct 2016 18:32:26 GMT

←Older revision		Revision as of 18:32, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j9u is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the NuA4 core complex==
		+	<StructureSection load='5j9u' size='340' side='right' caption='[[5j9u]], [[Resolution\|resolution]] 2.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5j9u]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J9U FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j9w\|5j9w]], [[5j9t\|5j9t]], [[5j9q\|5j9q]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=5j9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j9u OCA], [http://pdbe.org/5j9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j9u RCSB], [http://www.ebi.ac.uk/pdbsum/5j9u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j9u ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YNG2_YEAST YNG2_YEAST]] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. Involved in cell cycle progression and meiosis.<ref>PMID:10805724</ref> <ref>PMID:11544250</ref> <ref>PMID:11604499</ref> <ref>PMID:12417725</ref> [[http://www.uniprot.org/uniprot/ESA1_YEAST ESA1_YEAST]] Catalytic component of the NuA4 histone acetyltransferase (HAT) complex which is involved in epigenetic transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4, H3, H2B, H2A and H2A variant H2A.Z. Acetylates histone H4 to form H4K5ac, H4K8ac, H4K12ac and H4K16ac, histone H3 to form H3K14ac, histone H2B to form H2BK16ac, histone H2A to form H2AK4ac and H2AK7ac, and histone variant H2A.Z to form H2A.ZK14ac. Acetylation of histone H4 is essential for DNA double-strand break repair through homologous recombination. Involved in cell cycle progression. Recruitment to promoters depends on H3K4me.<ref>PMID:9858608</ref> <ref>PMID:10082517</ref> <ref>PMID:10835360</ref> <ref>PMID:10911987</ref> <ref>PMID:12353039</ref> <ref>PMID:15175650</ref> <ref>PMID:15494307</ref> <ref>PMID:15045029</ref> <ref>PMID:15923609</ref> [[http://www.uniprot.org/uniprot/EPL1_YEAST EPL1_YEAST]] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. Involved in gene silencing by neighboring heterochromatin, blockage of the silencing spreading along the chromosome, and required for cell cycle progression through G2/M.<ref>PMID:10911987</ref> <ref>PMID:12782659</ref> <ref>PMID:14966276</ref> <ref>PMID:15045029</ref> [[http://www.uniprot.org/uniprot/EAF6_YEAST EAF6_YEAST]] Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. Component of the NuA3 histone acetyltransferase complex, that acetylates Lys-14 of histone H3. Recruitment of NuA3 to nucleosomes requires methylated histone H3. In conjunction with the FACT complex, NuA3 may be involved in transcriptional regulation.<ref>PMID:17157260</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal structures of the NuA4 core complex and a cryoelectron microscopy structure with the nucleosome. The structures show that the histone-binding pocket of the enzyme is rearranged, suggesting its activation. The enzyme binds the histone tail mainly through the target lysine residue, with a preference for a small residue at the -1 position. The complex engages the nucleosome at the dish face and orients its catalytic pocket close to the H4 tail to achieve selective acetylation. The combined data reveal a space-sequence double recognition mechanism of the histone tails by a modifying enzyme in the context of the nucleosome.

-	~~Authors:~~ Chen, Z.C., ~~Xu, P~~.	+	The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism.,Xu P, Li C, Chen Z, Jiang S, Fan S, Wang J, Dai J, Zhu P, Chen Z Mol Cell. 2016 Sep 15;63(6):965-75. doi: 10.1016/j.molcel.2016.07.024. Epub 2016 , Sep 1. PMID:27594449<ref>PMID:27594449</ref>

-	~~Description: Crystal structure~~ of the ~~NuA4 core complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5j9u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histone acetyltransferase]]
		+	[[Category: Chen, Z C]]
	[[Category: Xu, P]]		[[Category: Xu, P]]
-	[[Category: ~~Chen, Z.C~~]]	+	[[Category: Acetylation]]
		+	[[Category: Histone]]
		+	[[Category: Nua4]]
		+	[[Category: Nucleosome]]
		+	[[Category: Transferase]]

OCA: Protected "5j9u" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:44:11 GMT

Protected "5j9u" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:44, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j9u is ON HOLD until Paper Publication Authors: Chen, Z.C., Xu, P. Description: Crystal structure of the NuA4 core complex [[Category: Unreleased ...

OCA — Wed, 11 May 2016 01:44:09 GMT

New page: '''Unreleased structure''' The entry 5j9u is ON HOLD until Paper Publication Authors: Chen, Z.C., Xu, P. Description: Crystal structure of the NuA4 core complex [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 5j9u is ON HOLD until Paper Publication

Authors: Chen, Z.C., Xu, P.

Description: Crystal structure of the NuA4 core complex
[[Category: Unreleased Structures]]
[[Category: Xu, P]]
[[Category: Chen, Z.C]]