6mr4 - Revision history

OCA at 06:37, 11 October 2023

2023-10-11T06:37:17Z

←Older revision		Revision as of 06:37, 11 October 2023
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	<StructureSection load='6mr4' size='340' side='right'caption='[[6mr4]], [[Resolution\|resolution]] 2.71Å' scene=''>		<StructureSection load='6mr4' size='340' side='right'caption='[[6mr4]], [[Resolution\|resolution]] 2.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mr4]] is a 6 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=6MR4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mr4]] is a 6 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=6MR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MR4 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>STH1, NPS1, YIL126W ([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">X-ray diffraction, [[Resolution\|Resolution]] 2.71Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~http://en.wikipedia.org/wiki/DNA_helicase DNA helicase~~]~~, with EC number [http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=6mr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mr4 OCA], [https://pdbe.org/6mr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mr4 RCSB], [https://www.ebi.ac.uk/pdbsum/6mr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mr4 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=6mr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mr4 OCA], [~~http~~://pdbe.org/6mr4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mr4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mr4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mr4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/STH1_YEAST STH1_YEAST]] Catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is the essential ATPase of the complex. It is a DNA translocase capable of nucleosome remodeling. Required for full expression of early meiotic genes. Essential for mitotic growth and repression of CHA1 expression. Also involved in G2 phase control.<ref>PMID:10025404</ref> <ref>PMID:10320476</ref> <ref>PMID:10329629</ref> <ref>PMID:12072455</ref> <ref>PMID:12183366</ref> <ref>PMID:12697820</ref> <ref>PMID:8980231</ref> <ref>PMID:9799253</ref>	+	[https://www.uniprot.org/uniprot/STH1_YEAST STH1_YEAST] Catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is the essential ATPase of the complex. It is a DNA translocase capable of nucleosome remodeling. Required for full expression of early meiotic genes. Essential for mitotic growth and repression of CHA1 expression. Also involved in G2 phase control.<ref>PMID:10025404</ref> <ref>PMID:10320476</ref> <ref>PMID:10329629</ref> <ref>PMID:12072455</ref> <ref>PMID:12183366</ref> <ref>PMID:12697820</ref> <ref>PMID:8980231</ref> <ref>PMID:9799253</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6mr4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6mr4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
-	[[Category: DNA helicase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Blus, B J~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Debler, E W~~]]	+	[[Category: Blus BJ]]
-	[[Category: ~~Hashimoto, H~~]]	+	[[Category: Debler EW]]
-	[[Category: ~~Krolak, A]]~~	+	[[Category: Hashimoto H]]
-	~~[[Category: Seo,~~ H S]]	+	[[Category: Krolak A]]
-	[[Category: ~~Acetylated-lysine histone binding~~]]	+	[[Category: Seo HS]]
-	[[Category: ~~Bromodomain]]~~	+
-	~~[[Category: Chromatin structure]]~~	+
-	~~[[Category: Gene expression]]~~	+
-	~~[[Category: Gene regulation~~]]	+

OCA at 06:18, 7 August 2019

2019-08-07T06:18:50Z

←Older revision		Revision as of 06:18, 7 August 2019
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	<StructureSection load='6mr4' size='340' side='right'caption='[[6mr4]], [[Resolution\|resolution]] 2.71Å' scene=''>		<StructureSection load='6mr4' size='340' side='right'caption='[[6mr4]], [[Resolution\|resolution]] 2.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mr4]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mr4]] is a 6 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=6MR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MR4 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STH1, NPS1, YIL126W ([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/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=6mr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mr4 OCA], [http://pdbe.org/6mr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mr4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mr4 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=6mr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mr4 OCA], [http://pdbe.org/6mr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mr4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mr4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/STH1_YEAST STH1_YEAST]] Catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is the essential ATPase of the complex. It is a DNA translocase capable of nucleosome remodeling. Required for full expression of early meiotic genes. Essential for mitotic growth and repression of CHA1 expression. Also involved in G2 phase control.<ref>PMID:10025404</ref> <ref>PMID:10320476</ref> <ref>PMID:10329629</ref> <ref>PMID:12072455</ref> <ref>PMID:12183366</ref> <ref>PMID:12697820</ref> <ref>PMID:8980231</ref> <ref>PMID:9799253</ref>		[[http://www.uniprot.org/uniprot/STH1_YEAST STH1_YEAST]] Catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is the essential ATPase of the complex. It is a DNA translocase capable of nucleosome remodeling. Required for full expression of early meiotic genes. Essential for mitotic growth and repression of CHA1 expression. Also involved in G2 phase control.<ref>PMID:10025404</ref> <ref>PMID:10320476</ref> <ref>PMID:10329629</ref> <ref>PMID:12072455</ref> <ref>PMID:12183366</ref> <ref>PMID:12697820</ref> <ref>PMID:8980231</ref> <ref>PMID:9799253</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bromodomains recognize a wide range of acetylated lysines in histones and other nuclear proteins. Substrate specificity is critical for their biological function and arises from unique acetyl-lysine binding sites formed by variable loop regions. Here, we analyzed substrate affinity and specificity of the yeast ScSth1p bromodomain, an essential component of the "Remodels the Structure of Chromatin" complex, and found that the wild-type bromodomain preferentially recognizes H3K14ac and H4K20ac peptides. Mutagenesis studies-guided by our crystal structure determined at 2.7-A resolution-revealed loop residues Ser1276 and Trp1338 as key determinants for such interactions. Strikingly, point mutations of each of these residues substantially increased peptide binding affinity and selectivity, respectively. Our data demonstrate that the ScSth1p bromodomain is not optimized for binding to an individual acetylation mark, but fine-tuned for interactions with several such modifications, consistent with the versatile and multivalent nature of histone recognition by reader modules such as bromodomains.
		+
		+	Substrate Affinity and Specificity of the ScSth1p Bromodomain Are Fine-Tuned for Versatile Histone Recognition.,Blus BJ, Hashimoto H, Seo HS, Krolak A, Debler EW Structure. 2019 Jul 9. pii: S0969-2126(19)30208-4. doi:, 10.1016/j.str.2019.06.009. PMID:31327661<ref>PMID:31327661</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mr4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: DNA helicase]]		[[Category: DNA helicase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:15, 24 July 2019

2019-07-24T06:15:00Z

←Older revision		Revision as of 06:15, 24 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mr4 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the Sth1 bromodomain from S.cerevisiae==
-		+	<StructureSection load='6mr4' size='340' side='right'caption='[[6mr4]], [[Resolution\|resolution]] 2.71Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mr4]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MR4 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></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=6mr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mr4 OCA], [http://pdbe.org/6mr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mr4 RCSB], [http://www.ebi.ac.uk/pdbsum/6mr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mr4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/STH1_YEAST STH1_YEAST]] Catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is the essential ATPase of the complex. It is a DNA translocase capable of nucleosome remodeling. Required for full expression of early meiotic genes. Essential for mitotic growth and repression of CHA1 expression. Also involved in G2 phase control.<ref>PMID:10025404</ref> <ref>PMID:10320476</ref> <ref>PMID:10329629</ref> <ref>PMID:12072455</ref> <ref>PMID:12183366</ref> <ref>PMID:12697820</ref> <ref>PMID:8980231</ref> <ref>PMID:9799253</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA helicase]]
		+	[[Category: Large Structures]]
		+	[[Category: Blus, B J]]
		+	[[Category: Debler, E W]]
		+	[[Category: Hashimoto, H]]
		+	[[Category: Krolak, A]]
		+	[[Category: Seo, H S]]
		+	[[Category: Acetylated-lysine histone binding]]
		+	[[Category: Bromodomain]]
		+	[[Category: Chromatin structure]]
		+	[[Category: Gene expression]]
		+	[[Category: Gene regulation]]

OCA at 05:29, 31 October 2018

2018-10-31T05:29:06Z

←Older revision		Revision as of 05:29, 31 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6mr4 is ON HOLD	+	The entry 6mr4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6mr4" [edit=sysop:move=sysop]

2018-10-17T06:41:13Z

Protected "6mr4" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:41, 17 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mr4 is ON HOLD Authors: Description: Category: Unreleased Structures

2018-10-17T06:41:12Z

New page: '''Unreleased structure''' The entry 6mr4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6mr4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]