8spu - Revision history

OCA at 08:23, 7 February 2024

OCA — Wed, 07 Feb 2024 08:23:55 GMT

←Older revision		Revision as of 08:23, 7 February 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A376KDN7_ECOLX A0A376KDN7_ECOLX] Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Binds maltose and higher maltodextrins.[RuleBase:RU365005][https://www.uniprot.org/uniprot/PO5F1_HUMAN PO5F1_HUMAN] Transcription factor that binds to the octamer motif (5'-ATTTGCAT-3'). Forms a trimeric complex with SOX2 or SOX15 on DNA and controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206. Critical for early embryogenesis and for embryonic stem cell pluripotency.<ref>PMID:18035408</ref>		[https://www.uniprot.org/uniprot/A0A376KDN7_ECOLX A0A376KDN7_ECOLX] Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Binds maltose and higher maltodextrins.[RuleBase:RU365005][https://www.uniprot.org/uniprot/PO5F1_HUMAN PO5F1_HUMAN] Transcription factor that binds to the octamer motif (5'-ATTTGCAT-3'). Forms a trimeric complex with SOX2 or SOX15 on DNA and controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206. Critical for early embryogenesis and for embryonic stem cell pluripotency.<ref>PMID:18035408</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap approximately 25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin.

-	Structural mechanism of LIN28B nucleosome targeting by OCT4.,Guan R, Lian T, Zhou BR, Wheeler D, Bai Y Mol Cell. 2023 Jun 15;83(12):1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. PMID:37327775<ref>PMID:37327775</ref>	+	==See Also==
-		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 8spu" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:22, 28 June 2023

OCA — Wed, 28 Jun 2023 21:22:13 GMT

←Older revision		Revision as of 21:22, 28 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8spu is ~~ON HOLD until Paper~~ Publication	+	==Structure of ESRRB nucleosome bound OCT4 at site c==
		+	<StructureSection load='8spu' size='340' side='right'caption='[[8spu]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8spu]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SPU FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 2.8Å</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=8spu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8spu OCA], [https://pdbe.org/8spu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8spu RCSB], [https://www.ebi.ac.uk/pdbsum/8spu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8spu ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A376KDN7_ECOLX A0A376KDN7_ECOLX] Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Binds maltose and higher maltodextrins.[RuleBase:RU365005][https://www.uniprot.org/uniprot/PO5F1_HUMAN PO5F1_HUMAN] Transcription factor that binds to the octamer motif (5'-ATTTGCAT-3'). Forms a trimeric complex with SOX2 or SOX15 on DNA and controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206. Critical for early embryogenesis and for embryonic stem cell pluripotency.<ref>PMID:18035408</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap approximately 25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin.

-	~~Authors~~:	+	Structural mechanism of LIN28B nucleosome targeting by OCT4.,Guan R, Lian T, Zhou BR, Wheeler D, Bai Y Mol Cell. 2023 Jun 15;83(12):1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. PMID:37327775<ref>PMID:37327775</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8spu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Ruifang G]]
		+	[[Category: Tengfei L]]
		+	[[Category: Yawen B]]

OCA at 04:26, 7 June 2023

OCA — Wed, 07 Jun 2023 04:26:46 GMT

←Older revision		Revision as of 04:26, 7 June 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8spu is ON HOLD	+	The entry 8spu is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8spu" [edit=sysop:move=sysop]

OCA — Wed, 10 May 2023 05:26:54 GMT

Protected "8spu" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:26, 10 May 2023

OCA: New page: '''Unreleased structure''' The entry 8spu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 May 2023 05:26:53 GMT

New page: '''Unreleased structure''' The entry 8spu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8spu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]