OCA at 17:16, 29 November 2023

OCA — Wed, 29 Nov 2023 17:16:05 GMT

←Older revision		Revision as of 17:16, 29 November 2023
Line 1:		Line 1:

-	====	+	==Crystal structure of BAZ2A with DNA==
-	<StructureSection load='7fhj' size='340' side='right'caption='[[7fhj]]' scene=''>	+	<StructureSection load='7fhj' size='340' side='right'caption='[[7fhj]], [[Resolution\|resolution]] 2.28Å' 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'>[[7fhj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FHJ 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=7fhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fhj OCA], [https://pdbe.org/7fhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fhj RCSB], [https://www.ebi.ac.uk/pdbsum/7fhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fhj 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]] 2.28Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=7fhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fhj OCA], [https://pdbe.org/7fhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fhj RCSB], [https://www.ebi.ac.uk/pdbsum/7fhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fhj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BAZ2A_HUMAN BAZ2A_HUMAN] Essential component of the NoRC (nucleolar remodeling complex) complex, a complex that mediates silencing of a fraction of rDNA by recruiting histone-modifying enzymes and DNA methyltransferases, leading to heterochromatin formation and transcriptional silencing. In the complex, it plays a central role by being recruited to rDNA and by targeting chromatin modifying enzymes such as HDAC1, leading to repress RNA polymerase I transcription. Recruited to rDNA via its interaction with TTF1 and its ability to recognize and bind histone H4 acetylated on 'Lys-16' (H4K16ac), leading to deacetylation of H4K5ac, H4K8ac, H4K12ac but not H4K16ac. Specifically binds pRNAs, 150-250 nucleotide RNAs that are complementary in sequence to the rDNA promoter; pRNA-binding is required for heterochromatin formation and rDNA silencing (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) (also called transcription termination factor-1 interacting protein 5), a key component of the nucleolar remodeling complex, recruits the nucleolar remodeling complex to ribosomal RNA genes, leading to their transcriptional repression. In addition to its tandem plant homeodomain-bromodomain that is involved in binding to acetylated histone H4, BAZ2A also contains a methyl-CpG-binding domain (MBD)-like Tip5/ARBP/MBD (TAM) domain that shares sequence homology with the MBD. In contrast with the methyl-CpG-binding ability of the canonical MBD, the BAZ2A TAM domain has been shown to bind to promoter-associated RNAs of ribosomal RNA genes and promoter DNAs of other genes independent of DNA methylation. Nevertheless, how the TAM domain binds to RNA/DNA mechanistically remains elusive. Here, we characterized the DNA-/RNA-binding basis of the BAZ2A TAM domain by EMSAs, isothermal titration calorimetry binding assays, mutagenesis analysis, and X-ray crystallography. Our results showed that the TAM domain of BAZ2A selectively binds to dsDNA and dsRNA and that it binds to the backbone of dsDNA in a sequence nonspecific manner, which is distinct from the base-specific binding of the canonical MBD. Thus, our results explain why the TAM domain of BAZ2A does not specifically bind to mCG or TG dsDNA like the canonical MBD and also provide insights for further biological study of BAZ2A acting as a transcription factor in the future.
		+
		+	Structural basis of the TAM domain of BAZ2A in binding to DNA or RNA independent of methylation status.,Chen S, Zhou M, Dong A, Loppnau P, Wang M, Min J, Liu K J Biol Chem. 2021 Dec;297(6):101351. doi: 10.1016/j.jbc.2021.101351. Epub 2021, Oct 27. PMID:34715126<ref>PMID:34715126</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7fhj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain adjacent to zinc finger 3D structures\|Bromodomain adjacent to zinc finger 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Arrowsmith CH]]
		+	[[Category: Dong A]]
		+	[[Category: Edwards AM]]
		+	[[Category: Li Y]]
		+	[[Category: Liu K]]
		+	[[Category: Loppnau P]]
		+	[[Category: Min J]]
		+	[[Category: Structural genomic]]

OCA at 14:08, 29 December 2021

OCA — Wed, 29 Dec 2021 14:08:47 GMT

←Older revision		Revision as of 14:08, 29 December 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7fhj ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7fhj' size='340' side='right'caption='[[7fhj]]' scene=''>
-	~~Authors~~: ~~Liu, K~~.~~, Dong, A~~.~~, Li, Y~~.~~, Loppnau, P~~.~~, Edwards, A~~.M.~~, Arrowsmith, C~~.~~H., Min, J., Structural Genomics Consortium, Structural Genomics Consortium (SGC)~~	+	== 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~~: ~~Crystal structure of BAZ2A with DNA~~	+	</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=7fhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fhj OCA], [https://pdbe.org/7fhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fhj RCSB], [https://www.ebi.ac.uk/pdbsum/7fhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fhj ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Loppnau~~, ~~P]]~~	+	__TOC__
-	[~~[Category~~: ~~Arrowsmith, C~~.H]]	+	</StructureSection>
-	[~~[Category~~: ~~Dong~~, ~~A]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Li, Y~~]]	+	[[Category: Z-disk]]
-	~~[[Category: Structural Genomics Consortium~~, ~~Structural Genomics Consortium (Sgc)]]~~	+
-	[~~[Category~~: ~~Liu, K]~~]	+
-	[[Category: ~~Min, J~~]]	+
-	[[Category: ~~Edwards, A.M~~]]	+

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

OCA — Wed, 04 Aug 2021 09:07:58 GMT

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

←Older revision

Revision as of 09:07, 4 August 2021

OCA: New page: '''Unreleased structure''' The entry 7fhj is ON HOLD Authors: Liu, K., Dong, A., Li, Y., Loppnau, P., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium, Structura...

OCA — Wed, 04 Aug 2021 09:07:57 GMT

New page: '''Unreleased structure''' The entry 7fhj is ON HOLD Authors: Liu, K., Dong, A., Li, Y., Loppnau, P., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium, Structura...

New page

'''Unreleased structure'''

The entry 7fhj is ON HOLD

Authors: Liu, K., Dong, A., Li, Y., Loppnau, P., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

Description: Crystal structure of BAZ2A with DNA
[[Category: Unreleased Structures]]
[[Category: Loppnau, P]]
[[Category: Arrowsmith, C.H]]
[[Category: Dong, A]]
[[Category: Li, Y]]
[[Category: Structural Genomics Consortium, Structural Genomics Consortium (Sgc)]]
[[Category: Liu, K]]
[[Category: Min, J]]
[[Category: Edwards, A.M]]

7fhj - Revision history

OCA at 17:16, 29 November 2023

OCA at 14:08, 29 December 2021

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

OCA: New page: '''Unreleased structure''' The entry 7fhj is ON HOLD Authors: Liu, K., Dong, A., Li, Y., Loppnau, P., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium, Structura...