OCA at 17:09, 29 November 2023

OCA — Wed, 29 Nov 2023 17:09:19 GMT

←Older revision		Revision as of 17:09, 29 November 2023
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-	====	+	==Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide==
-	<StructureSection load='7f4a' size='340' side='right'caption='[[7f4a]]' scene=''>	+	<StructureSection load='7f4a' size='340' side='right'caption='[[7f4a]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7f4a]] is a 2 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=7F4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F4A FirstGlance]. <br>
-	</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=7f4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4a OCA], [https://pdbe.org/7f4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4a RCSB], [https://www.ebi.ac.uk/pdbsum/7f4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4a ProSAT]</span></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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=LBZ:(2~{S})-2-azanyl-6-benzamido-hexanoic+acid'>LBZ</scene></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=7f4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4a OCA], [https://pdbe.org/7f4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4a RCSB], [https://www.ebi.ac.uk/pdbsum/7f4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4a ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TAF14_YEAST TAF14_YEAST] Functions as a component of the DNA-binding general transcription factor complex TFIID, the RNA polymerase II associated general transcription factor complex TFIIF, and the chromatin-remodeling complex SWI/SNF. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. TFIIF is essential for the initiation of transcription by RNA polymerase II. TFIIF functions include the recruitment of RNA polymerase II to the promoter bound DNA-TBP-TFIIB complex, decreasing the affinity of RNA polymerase II for non-specific DNA, allowing for the subsequent recruitment of TFIIE and TFIIH, and facilitating RNA polymerase II elongation. The TAF14 subunit has stimulatory activity. Component of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, is required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors. Component of the histone acetyltransferase NuA3 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:9618449</ref> <ref>PMID:10788514</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> <ref>PMID:12672490</ref> <ref>PMID:17157260</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lysine benzoylation (Kbz) is a recently discovered post-translational modification associated with active transcription. However, the proteins for maintaining and interpreting Kbz and the physiological roles of Kbz remain elusive. Here, we systematically characterize writer, eraser, and reader proteins of histone Kbz in S. cerevisiae using proteomic, biochemical, and structural approaches. Our study identifies 27 Kbz sites on yeast histones that can be regulated by cellular metabolic states. The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex and NAD(+)-dependent histone deacetylase Hst2 could function as the writer and eraser of histone Kbz, respectively. Crystal structures of Hst2 complexes reveal the molecular basis for Kbz recognition and catalysis by Hst2. In addition, we demonstrate that a subset of YEATS domains and bromodomains serve as Kbz readers, and structural analyses reveal how YEATS and bromodomains recognize Kbz marks. Moreover, the proteome-wide screening of Kbz-modified proteins identifies 207 Kbz sites on 149 non-histone proteins enriched in ribosome biogenesis, glycolysis/gluconeogenesis, and rRNA processing pathways. Our studies identify regulatory elements for the Kbz pathway and provide a framework for dissecting the biological functions of lysine benzoylation.
		+
		+	Global profiling of regulatory elements in the histone benzoylation pathway.,Wang D, Yan F, Wu P, Ge K, Li M, Li T, Gao Y, Peng C, Chen Y Nat Commun. 2022 Mar 16;13(1):1369. doi: 10.1038/s41467-022-29057-2. PMID:35296687<ref>PMID:35296687</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7f4a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Wang D]]
		+	[[Category: Yan F]]
		+	[[Category: Yong C]]

OCA at 06:13, 16 March 2022

OCA — Wed, 16 Mar 2022 06:13:04 GMT

←Older revision		Revision as of 06:13, 16 March 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7f4a ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7f4a' size='340' side='right'caption='[[7f4a]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7f4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f4a OCA], [https://pdbe.org/7f4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f4a RCSB], [https://www.ebi.ac.uk/pdbsum/7f4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f4a ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 08:39, 7 July 2021

OCA — Wed, 07 Jul 2021 08:39:54 GMT

←Older revision		Revision as of 08:39, 7 July 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7f4a is ON HOLD	+	The entry 7f4a is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7f4a" [edit=sysop:move=sysop]

OCA — Fri, 25 Jun 2021 06:08:09 GMT

Protected "7f4a" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:08, 25 June 2021

OCA: New page: '''Unreleased structure''' The entry 7f4a is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 25 Jun 2021 06:08:08 GMT

New page: '''Unreleased structure''' The entry 7f4a is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7f4a is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7f4a - Revision history

OCA at 17:09, 29 November 2023

OCA at 06:13, 16 March 2022

OCA at 08:39, 7 July 2021

OCA: Protected "7f4a" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7f4a is ON HOLD Authors: Description: Category: Unreleased Structures