5ojs - Revision history

OCA at 16:52, 13 December 2023

OCA — Wed, 13 Dec 2023 16:52:22 GMT

←Older revision		Revision as of 16:52, 13 December 2023
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	<SX load='5ojs' size='340' side='right' viewer='molstar' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>		<SX load='5ojs' size='340' side='right' viewer='molstar' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OJS FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~TRA1~~, ~~YHR099W (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=559292 Baker's yeast])~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.7Å</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=5ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ojs OCA], [~~http~~://pdbe.org/5ojs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ojs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ojs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ojs 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=5ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ojs OCA], [https://pdbe.org/5ojs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ojs RCSB], [https://www.ebi.ac.uk/pdbsum/5ojs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ojs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TRA1_YEAST TRA1_YEAST]] Essential component of histone acetyltransferase (HAT) complexes, which serves as a target for activators during recruitment of HAT complexes. Essential for vegetative growth. Functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:11423663</ref>	+	[https://www.uniprot.org/uniprot/TRA1_YEAST TRA1_YEAST] Essential component of histone acetyltransferase (HAT) complexes, which serves as a target for activators during recruitment of HAT complexes. Essential for vegetative growth. Functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:11423663</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__
	</SX>		</SX>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aciyan, E]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Cheung~~, A C.M~~]]	+	[[Category: Aciyan E]]
-	[[Category: Diaz-Santin~~, L M~~]]	+	[[Category: Cheung ACM]]
-	[[Category: Lukoyanova, N]]	+	[[Category: Diaz-Santin LM]]
-	~~[[Category: Coactivator]]~~	+	[[Category: Lukoyanova N]]
-	~~[[Category: Nua4]]~~	+
-	~~[[Category: Pikk]]~~	+
-	~~[[Category: Saga]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 21:28, 10 April 2020

OCA — Fri, 10 Apr 2020 21:28:49 GMT

←Older revision		Revision as of 21:28, 10 April 2020
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	<SX load='5ojs' size='340' side='right' viewer='molstar' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>		<SX load='5ojs' size='340' side='right' viewer='molstar' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OJS FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRA1, YHR099W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRA1, YHR099W ([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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ojs OCA], [http://pdbe.org/5ojs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ojs RCSB], [http://www.ebi.ac.uk/pdbsum/5ojs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ojs 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=5ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ojs OCA], [http://pdbe.org/5ojs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ojs RCSB], [http://www.ebi.ac.uk/pdbsum/5ojs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ojs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:24, 6 March 2020

OCA — Fri, 06 Mar 2020 19:24:20 GMT

←Older revision		Revision as of 19:24, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1==		==Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1==
-	<~~StructureSection~~ load='5ojs' size='340' side='right'caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>	+	<SX load='5ojs' size='340' side='right' viewer='molstar' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OJS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OJS FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 16:49, 11 December 2019

OCA — Wed, 11 Dec 2019 16:49:41 GMT

←Older revision		Revision as of 16:49, 11 December 2019
Line 1:		Line 1:

	==Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1==		==Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1==
-	<StructureSection load='5ojs' size='340' side='right' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>	+	<StructureSection load='5ojs' size='340' side='right'caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OJS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OJS FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Aciyan, E]]		[[Category: Aciyan, E]]
	[[Category: Cheung, A C.M]]		[[Category: Cheung, A C.M]]

OCA at 07:01, 31 January 2018

OCA — Wed, 31 Jan 2018 07:01:59 GMT

←Older revision		Revision as of 07:01, 31 January 2018
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	<StructureSection load='5ojs' size='340' side='right' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>		<StructureSection load='5ojs' size='340' side='right' caption='[[5ojs]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ojs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ojs]] is a 1 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=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OJS FirstGlance]. <br>
-	</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=5ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ojs OCA], [http://pdbe.org/5ojs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ojs RCSB], [http://www.ebi.ac.uk/pdbsum/5ojs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ojs ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRA1, YHR099W ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ojs OCA], [http://pdbe.org/5ojs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ojs RCSB], [http://www.ebi.ac.uk/pdbsum/5ojs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ojs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Aciyan, E]]		[[Category: Aciyan, E]]
	[[Category: Cheung, A C.M]]		[[Category: Cheung, A C.M]]

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

OCA — Thu, 17 Aug 2017 05:56:32 GMT

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

←Older revision

Revision as of 05:56, 17 August 2017

OCA: New page: ==Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1== == Structural highlights ==
<table><tr><td colspan='2'>[[5ojs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OJS FirstGlance]. <br>
</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=5ojs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ojs OCA], [http://pdbe.org/5ojs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ojs RCSB], [http://www.ebi.ac.uk/pdbsum/5ojs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ojs ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/TRA1_YEAST TRA1_YEAST]] Essential component of histone acetyltransferase (HAT) complexes, which serves as a target for activators during recruitment of HAT complexes. Essential for vegetative growth. Functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:11423663</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Saccharomyces cerevsisae Tra1 to 3.7 A resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair. The structure was fitted into an existing SAGA EM reconstruction and reveals limited contact surfaces to Tra1, hence it does not act as a molecular scaffold within SAGA. Mutations that affect activator targeting are distributed across the Tra1 structure, but also cluster within the N-terminal Finger region, indicating the presence of an activator interaction site. The structure of Tra1 is a key milestone in deciphering the mechanism of multiple coactivator complexes.

Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution.,Diaz-Santin LM, Lukoyanova N, Aciyan E, Cheung AC Elife. 2017 Aug 2;6. pii: e28384. doi: 10.7554/eLife.28384. PMID:28767037<ref>PMID:28767037</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ojs" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Aciyan, E]]
[[Category: Cheung, A C.M]]
[[Category: Diaz-Santin, L M]]
[[Category: Lukoyanova, N]]
[[Category: Coactivator]]
[[Category: Nua4]]
[[Category: Pikk]]
[[Category: Saga]]
[[Category: Transcription]]