5yef - Revision history

OCA at 10:23, 27 March 2024

OCA — Wed, 27 Mar 2024 10:23:08 GMT

←Older revision		Revision as of 10:23, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5yef' size='340' side='right'caption='[[5yef]], [[Resolution\|resolution]] 2.81Å' scene=''>		<StructureSection load='5yef' size='340' side='right'caption='[[5yef]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yef]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YEF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yef]] is a 12 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=5YEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YEF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ZN:ZINC+ION'>ZN</scene~~></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]] 2.807Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CTCF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5yef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yef OCA], [~~http~~://pdbe.org/5yef PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yef RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yef PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yef 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=5yef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yef OCA], [https://pdbe.org/5yef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yef RCSB], [https://www.ebi.ac.uk/pdbsum/5yef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yef ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CTCF_HUMAN CTCF_HUMAN]] Chromatin binding factor that binds to DNA sequence specific sites. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Acts as transcriptional repressor binding to promoters of vertebrate MYC gene and BAG1 gene. Also binds to the PLK and PIM1 promoters. Acts as a transcriptional activator of APP. Regulates APOA1/C3/A4/A5 gene cluster and controls MHC class II gene expression. Plays an essential role in oocyte and preimplantation embryo development by activating or repressing transcription. Seems to act as tumor suppressor. Plays a critical role in the epigenetic regulation. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, binding within the H19 imprinting control region (ICR) mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to IGF2. Plays a critical role in gene silencing over considerable distances in the genome. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation and maintaining methylation-free zones. Inversely, binding to target sites is prevented by CpG methylation. Plays a important role in chromatin remodeling. Can dimerize when it is bound to different DNA sequences, mediating long-range chromatin looping. Mediates interchromosomal association between IGF2/H19 and WSB1/NF1 and may direct distant DNA segments to a common transcription factory. Causes local loss of histone acetylation and gain of histone methylation in the beta-globin locus, without affecting transcription. When bound to chromatin, it provides an anchor point for nucleosomes positioning. Seems to be essential for homologous X-chromosome pairing. May participate with Tsix in establishing a regulatable epigenetic switch for X chromosome inactivation. May play a role in preventing the propagation of stable methylation at the escape genes from X- inactivation. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Regulates asynchronous replication of IGF2/H19.<ref>PMID:8649389</ref> <ref>PMID:9591631</ref> <ref>PMID:11743158</ref> <ref>PMID:16815976</ref> <ref>PMID:17827499</ref> <ref>PMID:18413740</ref> <ref>PMID:18347100</ref> <ref>PMID:18654629</ref> <ref>PMID:18550811</ref> <ref>PMID:19322193</ref>	+	[https://www.uniprot.org/uniprot/CTCF_HUMAN CTCF_HUMAN] Chromatin binding factor that binds to DNA sequence specific sites. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Acts as transcriptional repressor binding to promoters of vertebrate MYC gene and BAG1 gene. Also binds to the PLK and PIM1 promoters. Acts as a transcriptional activator of APP. Regulates APOA1/C3/A4/A5 gene cluster and controls MHC class II gene expression. Plays an essential role in oocyte and preimplantation embryo development by activating or repressing transcription. Seems to act as tumor suppressor. Plays a critical role in the epigenetic regulation. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, binding within the H19 imprinting control region (ICR) mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to IGF2. Plays a critical role in gene silencing over considerable distances in the genome. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation and maintaining methylation-free zones. Inversely, binding to target sites is prevented by CpG methylation. Plays a important role in chromatin remodeling. Can dimerize when it is bound to different DNA sequences, mediating long-range chromatin looping. Mediates interchromosomal association between IGF2/H19 and WSB1/NF1 and may direct distant DNA segments to a common transcription factory. Causes local loss of histone acetylation and gain of histone methylation in the beta-globin locus, without affecting transcription. When bound to chromatin, it provides an anchor point for nucleosomes positioning. Seems to be essential for homologous X-chromosome pairing. May participate with Tsix in establishing a regulatable epigenetic switch for X chromosome inactivation. May play a role in preventing the propagation of stable methylation at the escape genes from X- inactivation. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Regulates asynchronous replication of IGF2/H19.<ref>PMID:8649389</ref> <ref>PMID:9591631</ref> <ref>PMID:11743158</ref> <ref>PMID:16815976</ref> <ref>PMID:17827499</ref> <ref>PMID:18413740</ref> <ref>PMID:18347100</ref> <ref>PMID:18654629</ref> <ref>PMID:18550811</ref> <ref>PMID:19322193</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	CTCF, a conserved 3D genome architecture protein, determines proper genome-wide chromatin looping interactions through directional binding to specific sequence elements of four modules within numerous CTCF-binding sites (CBSs) by its 11 zinc fingers (ZFs). Here, we report four crystal structures of human CTCF in complex with CBSs of the protocadherin (Pcdh) clusters. We show that directional CTCF binding to cognate CBSs of the Pcdh enhancers and promoters is achieved through inserting its ZF3, ZFs 4-7, and ZFs 9-11 into the major groove along CBSs, resulting in a sequence-specific recognition of module 4, modules 3 and 2, and module 1, respectively; and ZF8 serves as a spacer element for variable distances between modules 1 and 2. In addition, the base contact with the asymmetric "A" in the central position of modules 2-3, is essential for directional recognition of the CBSs with symmetric core sequences but lacking module 1. Furthermore, CTCF tolerates base changes at specific positions within the degenerated CBS sequences, permitting genome-wide CTCF binding to a diverse range of CBSs. Together, these complex structures provide important insights into the molecular mechanisms for the directionality, diversity, flexibility, dynamics, and conservation of multivalent CTCF binding to its cognate sites across the entire human genome.	+
-		+
-	Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites.,Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y Cell Res. 2017 Nov;27(11):1365-1377. doi: 10.1038/cr.2017.131. Epub 2017 Oct 27. PMID:29076501<ref>PMID:29076501</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yef" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li, X]]	+	[[Category: Synthetic construct]]
-	[[Category: Wang, J]]	+	[[Category: Li X]]
-	[[Category: Wang, M]]	+	[[Category: Wang J]]
-	[[Category: Wang, Y]]	+	[[Category: Wang M]]
-	[[Category: Yin, M]]	+	[[Category: Wang Y]]
-	~~[[Category: 3d genome]]~~	+	[[Category: Yin M]]
-	~~[[Category: Contact loop]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Enhancer]]~~	+
-	~~[[Category: Higher-order chromatin structure]]~~	+
-	~~[[Category: Insulator]]~~	+
-	~~[[Category: Promoter]]~~	+
-	~~[[Category: Topological domain]]~~	+
-	~~[[Category: Zinc finger~~]]	+

OCA at 12:42, 25 December 2019

OCA — Wed, 25 Dec 2019 12:42:22 GMT

←Older revision		Revision as of 12:42, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of CTCF ZFs2-8-Hs5-1aE==		==Crystal structure of CTCF ZFs2-8-Hs5-1aE==
-	<StructureSection load='5yef' size='340' side='right' caption='[[5yef]], [[Resolution\|resolution]] 2.81Å' scene=''>	+	<StructureSection load='5yef' size='340' side='right'caption='[[5yef]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yef]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YEF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yef]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YEF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CTCF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5yef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yef OCA], [http://pdbe.org/5yef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yef RCSB], [http://www.ebi.ac.uk/pdbsum/5yef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yef 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=5yef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yef OCA], [http://pdbe.org/5yef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yef RCSB], [http://www.ebi.ac.uk/pdbsum/5yef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yef ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Li, X]]		[[Category: Li, X]]
	[[Category: Wang, J]]		[[Category: Wang, J]]

OCA at 06:14, 29 November 2017

OCA — Wed, 29 Nov 2017 06:14:14 GMT

←Older revision		Revision as of 06:14, 29 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yef is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of CTCF ZFs2-8-Hs5-1aE==
		+	<StructureSection load='5yef' size='340' side='right' caption='[[5yef]], [[Resolution\|resolution]] 2.81Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yef]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YEF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5yef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yef OCA], [http://pdbe.org/5yef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yef RCSB], [http://www.ebi.ac.uk/pdbsum/5yef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yef ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CTCF_HUMAN CTCF_HUMAN]] Chromatin binding factor that binds to DNA sequence specific sites. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Acts as transcriptional repressor binding to promoters of vertebrate MYC gene and BAG1 gene. Also binds to the PLK and PIM1 promoters. Acts as a transcriptional activator of APP. Regulates APOA1/C3/A4/A5 gene cluster and controls MHC class II gene expression. Plays an essential role in oocyte and preimplantation embryo development by activating or repressing transcription. Seems to act as tumor suppressor. Plays a critical role in the epigenetic regulation. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, binding within the H19 imprinting control region (ICR) mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to IGF2. Plays a critical role in gene silencing over considerable distances in the genome. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation and maintaining methylation-free zones. Inversely, binding to target sites is prevented by CpG methylation. Plays a important role in chromatin remodeling. Can dimerize when it is bound to different DNA sequences, mediating long-range chromatin looping. Mediates interchromosomal association between IGF2/H19 and WSB1/NF1 and may direct distant DNA segments to a common transcription factory. Causes local loss of histone acetylation and gain of histone methylation in the beta-globin locus, without affecting transcription. When bound to chromatin, it provides an anchor point for nucleosomes positioning. Seems to be essential for homologous X-chromosome pairing. May participate with Tsix in establishing a regulatable epigenetic switch for X chromosome inactivation. May play a role in preventing the propagation of stable methylation at the escape genes from X- inactivation. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Regulates asynchronous replication of IGF2/H19.<ref>PMID:8649389</ref> <ref>PMID:9591631</ref> <ref>PMID:11743158</ref> <ref>PMID:16815976</ref> <ref>PMID:17827499</ref> <ref>PMID:18413740</ref> <ref>PMID:18347100</ref> <ref>PMID:18654629</ref> <ref>PMID:18550811</ref> <ref>PMID:19322193</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CTCF, a conserved 3D genome architecture protein, determines proper genome-wide chromatin looping interactions through directional binding to specific sequence elements of four modules within numerous CTCF-binding sites (CBSs) by its 11 zinc fingers (ZFs). Here, we report four crystal structures of human CTCF in complex with CBSs of the protocadherin (Pcdh) clusters. We show that directional CTCF binding to cognate CBSs of the Pcdh enhancers and promoters is achieved through inserting its ZF3, ZFs 4-7, and ZFs 9-11 into the major groove along CBSs, resulting in a sequence-specific recognition of module 4, modules 3 and 2, and module 1, respectively; and ZF8 serves as a spacer element for variable distances between modules 1 and 2. In addition, the base contact with the asymmetric "A" in the central position of modules 2-3, is essential for directional recognition of the CBSs with symmetric core sequences but lacking module 1. Furthermore, CTCF tolerates base changes at specific positions within the degenerated CBS sequences, permitting genome-wide CTCF binding to a diverse range of CBSs. Together, these complex structures provide important insights into the molecular mechanisms for the directionality, diversity, flexibility, dynamics, and conservation of multivalent CTCF binding to its cognate sites across the entire human genome.

-	~~Authors: Yin~~, M., Wang, J., Wang, M., Li, X., ~~Wang~~, Y.	+	Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites.,Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y Cell Res. 2017 Nov;27(11):1365-1377. doi: 10.1038/cr.2017.131. Epub 2017 Oct 27. PMID:29076501<ref>PMID:29076501</ref>

-	~~Description: Crystal structure~~ of ~~CTCF ZFs2~~-8-~~Hs5-1aE~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yef" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, X]]
		+	[[Category: Wang, J]]
	[[Category: Wang, M]]		[[Category: Wang, M]]
	[[Category: Wang, Y]]		[[Category: Wang, Y]]
	[[Category: Yin, M]]		[[Category: Yin, M]]
-	[[Category: ~~Wang, J~~]]	+	[[Category: 3d genome]]
-	[[Category: ~~Li, X~~]]	+	[[Category: Contact loop]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Enhancer]]
		+	[[Category: Higher-order chromatin structure]]
		+	[[Category: Insulator]]
		+	[[Category: Promoter]]
		+	[[Category: Topological domain]]
		+	[[Category: Zinc finger]]

OCA at 05:22, 11 October 2017

OCA — Wed, 11 Oct 2017 05:22:18 GMT

←Older revision		Revision as of 05:22, 11 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yef is ON HOLD	+	The entry 5yef is ON HOLD until Paper Publication

	Authors: Yin, M., Wang, J., Wang, M., Li, X., Wang, Y.		Authors: Yin, M., Wang, J., Wang, M., Li, X., Wang, Y.
Line 9:		Line 9:
	[[Category: Wang, M]]		[[Category: Wang, M]]
	[[Category: Wang, Y]]		[[Category: Wang, Y]]
-	[[Category: Wang, J]]
	[[Category: Yin, M]]		[[Category: Yin, M]]
		+	[[Category: Wang, J]]
	[[Category: Li, X]]		[[Category: Li, X]]

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

OCA — Wed, 27 Sep 2017 16:28:25 GMT

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

←Older revision

Revision as of 16:28, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yef is ON HOLD Authors: Yin, M., Wang, J., Wang, M., Li, X., Wang, Y. Description: Crystal structure of CTCF ZFs2-8-Hs5-1aE [[Category: Unreleased...

OCA — Wed, 27 Sep 2017 16:28:24 GMT

New page: '''Unreleased structure''' The entry 5yef is ON HOLD Authors: Yin, M., Wang, J., Wang, M., Li, X., Wang, Y. Description: Crystal structure of CTCF ZFs2-8-Hs5-1aE [[Category: Unreleased...

New page

'''Unreleased structure'''

The entry 5yef is ON HOLD

Authors: Yin, M., Wang, J., Wang, M., Li, X., Wang, Y.

Description: Crystal structure of CTCF ZFs2-8-Hs5-1aE
[[Category: Unreleased Structures]]
[[Category: Wang, M]]
[[Category: Wang, Y]]
[[Category: Wang, J]]
[[Category: Yin, M]]
[[Category: Li, X]]