6lff - Revision history

OCA at 10:59, 22 November 2023

OCA — Wed, 22 Nov 2023 10:59:17 GMT

←Older revision		Revision as of 10:59, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6lff' size='340' side='right'caption='[[6lff]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='6lff' size='340' side='right'caption='[[6lff]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lff]] is a 4 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=6LFF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LFF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lff]] 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=6LFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LFF FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</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]] 1.79Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o49\|2o49]], [[2o4a\|2o4a]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SATB1 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=6lff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lff OCA], [https://pdbe.org/6lff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lff RCSB], [https://www.ebi.ac.uk/pdbsum/6lff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lff ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6lff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lff OCA], [~~http~~://pdbe.org/6lff PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lff RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lff PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lff ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SATB1_HUMAN SATB1_HUMAN]] Crucial silencing factor contributing to the initiation of X inactivation mediated by Xist RNA that occurs during embryogenesis and in lymphoma (By similarity). Binds to DNA at special AT-rich sequences, the consensus SATB1-binding sequence (CSBS), at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcriptional repressor controlling nuclear and viral gene expression in a phosphorylated and acetylated status-dependent manner, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes (e.g. PML at the MHC-I locus) and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Modulates genes that are essential in the maturation of the immune T-cell CD8SP from thymocytes. Required for the switching of fetal globin species, and beta- and gamma-globin genes regulation during erythroid differentiation. Plays a role in chromatin organization and nuclear architecture during apoptosis. Interacts with the unique region (UR) of cytomegalovirus (CMV). Alu-like motifs and SATB1-binding sites provide a unique chromatin context which seems preferentially targeted by the HIV-1 integration machinery. Moreover, HIV-1 Tat may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T-cells by binding to the same domain than HDAC1. Delineates specific epigenetic modifications at target gene loci, directly up-regulating metastasis-associated genes while down-regulating tumor-suppressor genes. Reprograms chromatin organization and the transcription profiles of breast tumors to promote growth and metastasis.<ref>PMID:1505028</ref> <ref>PMID:9111059</ref> <ref>PMID:9548713</ref> <ref>PMID:10595394</ref> <ref>PMID:11463840</ref> <ref>PMID:12374985</ref> <ref>PMID:12692553</ref> <ref>PMID:15618465</ref> <ref>PMID:15713622</ref> <ref>PMID:16377216</ref> <ref>PMID:16630892</ref> <ref>PMID:17376900</ref> <ref>PMID:17173041</ref> <ref>PMID:18337816</ref> <ref>PMID:19332023</ref> <ref>PMID:19430959</ref> <ref>PMID:19103759</ref> <ref>PMID:19247486</ref>	+	[https://www.uniprot.org/uniprot/SATB1_HUMAN SATB1_HUMAN] Crucial silencing factor contributing to the initiation of X inactivation mediated by Xist RNA that occurs during embryogenesis and in lymphoma (By similarity). Binds to DNA at special AT-rich sequences, the consensus SATB1-binding sequence (CSBS), at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcriptional repressor controlling nuclear and viral gene expression in a phosphorylated and acetylated status-dependent manner, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes (e.g. PML at the MHC-I locus) and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Modulates genes that are essential in the maturation of the immune T-cell CD8SP from thymocytes. Required for the switching of fetal globin species, and beta- and gamma-globin genes regulation during erythroid differentiation. Plays a role in chromatin organization and nuclear architecture during apoptosis. Interacts with the unique region (UR) of cytomegalovirus (CMV). Alu-like motifs and SATB1-binding sites provide a unique chromatin context which seems preferentially targeted by the HIV-1 integration machinery. Moreover, HIV-1 Tat may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T-cells by binding to the same domain than HDAC1. Delineates specific epigenetic modifications at target gene loci, directly up-regulating metastasis-associated genes while down-regulating tumor-suppressor genes. Reprograms chromatin organization and the transcription profiles of breast tumors to promote growth and metastasis.<ref>PMID:1505028</ref> <ref>PMID:9111059</ref> <ref>PMID:9548713</ref> <ref>PMID:10595394</ref> <ref>PMID:11463840</ref> <ref>PMID:12374985</ref> <ref>PMID:12692553</ref> <ref>PMID:15618465</ref> <ref>PMID:15713622</ref> <ref>PMID:16377216</ref> <ref>PMID:16630892</ref> <ref>PMID:17376900</ref> <ref>PMID:17173041</ref> <ref>PMID:18337816</ref> <ref>PMID:19332023</ref> <ref>PMID:19430959</ref> <ref>PMID:19103759</ref> <ref>PMID:19247486</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Akutsu, Y]]	+	[[Category: Synthetic construct]]
-	[[Category: Kubota, T]]	+	[[Category: Akutsu Y]]
-	[[Category: Yamasaki, K]]	+	[[Category: Kubota T]]
-	[[Category: Yamasaki, T]]	+	[[Category: Yamasaki K]]
-	~~[[Category: Dna modification]]~~	+	[[Category: Yamasaki T]]
-	~~[[Category: Dna-binding protein]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 05:45, 13 May 2020

OCA — Wed, 13 May 2020 05:45:57 GMT

←Older revision		Revision as of 05:45, 13 May 2020
Line 3:		Line 3:
	<StructureSection load='6lff' size='340' side='right'caption='[[6lff]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='6lff' size='340' side='right'caption='[[6lff]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lff]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LFF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6LFF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lff]] is a 4 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=6LFF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LFF FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o49\|2o49]], [[2o4a\|2o4a]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o49\|2o49]], [[2o4a\|2o4a]]</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=6lff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lff OCA], [http://pdbe.org/6lff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lff RCSB], [http://www.ebi.ac.uk/pdbsum/6lff PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lff ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SATB1 ([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://proteopedia.org/fgij/fg.htm?mol=6lff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lff OCA], [http://pdbe.org/6lff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lff RCSB], [http://www.ebi.ac.uk/pdbsum/6lff PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lff ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Akutsu, Y]]		[[Category: Akutsu, Y]]

OCA at 09:10, 1 April 2020

OCA — Wed, 01 Apr 2020 09:10:00 GMT

←Older revision		Revision as of 09:10, 1 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6lff is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==transcription factor SATB1 CUTr1 domain in complex with a phosphorothioate DNA==
		+	<StructureSection load='6lff' size='340' side='right'caption='[[6lff]], [[Resolution\|resolution]] 1.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6lff]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LFF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6LFF FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o49\|2o49]], [[2o4a\|2o4a]]</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=6lff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lff OCA], [http://pdbe.org/6lff PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lff RCSB], [http://www.ebi.ac.uk/pdbsum/6lff PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lff ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SATB1_HUMAN SATB1_HUMAN]] Crucial silencing factor contributing to the initiation of X inactivation mediated by Xist RNA that occurs during embryogenesis and in lymphoma (By similarity). Binds to DNA at special AT-rich sequences, the consensus SATB1-binding sequence (CSBS), at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcriptional repressor controlling nuclear and viral gene expression in a phosphorylated and acetylated status-dependent manner, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes (e.g. PML at the MHC-I locus) and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Modulates genes that are essential in the maturation of the immune T-cell CD8SP from thymocytes. Required for the switching of fetal globin species, and beta- and gamma-globin genes regulation during erythroid differentiation. Plays a role in chromatin organization and nuclear architecture during apoptosis. Interacts with the unique region (UR) of cytomegalovirus (CMV). Alu-like motifs and SATB1-binding sites provide a unique chromatin context which seems preferentially targeted by the HIV-1 integration machinery. Moreover, HIV-1 Tat may overcome SATB1-mediated repression of IL2 and IL2RA (interleukin) in T-cells by binding to the same domain than HDAC1. Delineates specific epigenetic modifications at target gene loci, directly up-regulating metastasis-associated genes while down-regulating tumor-suppressor genes. Reprograms chromatin organization and the transcription profiles of breast tumors to promote growth and metastasis.<ref>PMID:1505028</ref> <ref>PMID:9111059</ref> <ref>PMID:9548713</ref> <ref>PMID:10595394</ref> <ref>PMID:11463840</ref> <ref>PMID:12374985</ref> <ref>PMID:12692553</ref> <ref>PMID:15618465</ref> <ref>PMID:15713622</ref> <ref>PMID:16377216</ref> <ref>PMID:16630892</ref> <ref>PMID:17376900</ref> <ref>PMID:17173041</ref> <ref>PMID:18337816</ref> <ref>PMID:19332023</ref> <ref>PMID:19430959</ref> <ref>PMID:19103759</ref> <ref>PMID:19247486</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphorothioate modification is commonly introduced into therapeutic oligonucleotides, typically as a racemic mixture in which either of the two non-bridging phosphate oxygens is replaced by sulfur, which frequently increases affinities with proteins. Here, we used isothermal titration calorimetry and X-ray crystallography to investigate the thermodynamic and structural properties of the interaction between the primary DNA-binding domain (CUTr1) of transcription factor SATB1 and dodecamer DNAs with racemic phosphorothioate modifications at the six sites known to contact CUTr1 directly. For both the modified and unmodified DNAs, the binding reactions were enthalpy-driven at a moderate salt concentration (50 mM NaCl), while being entropy-driven at higher salt concentrations with reduced affinities. The phosphorothioate modifications lowered this susceptibility to salt, resulting in a significantly enhanced affinity at a higher salt concentration (200 mM NaCl), although only some DNA molecular species remained interacting with CUTr1. This was explained by unequal populations of the two diastereomers in the crystal structure of the complex of CUTr1 and the phosphorothioate-modified DNA. The preferred diastereomer formed more hydrogen bonds with the oxygen atoms and/or more hydrophobic contacts with the sulfur atoms than the other, revealing the origins of the enhanced affinity.

-	~~Authors~~:	+	Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts.,Yamasaki K, Akutsu Y, Yamasaki T, Miyagishi M, Kubota T Nucleic Acids Res. 2020 Mar 18. pii: 5809661. doi: 10.1093/nar/gkaa170. PMID:32187371<ref>PMID:32187371</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6lff" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Akutsu, Y]]
		+	[[Category: Kubota, T]]
		+	[[Category: Yamasaki, K]]
		+	[[Category: Yamasaki, T]]
		+	[[Category: Dna modification]]
		+	[[Category: Dna-binding protein]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]
		+	[[Category: Transcription-dna complex]]

OCA at 05:38, 18 December 2019

OCA — Wed, 18 Dec 2019 05:38:04 GMT

←Older revision		Revision as of 05:38, 18 December 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 11 Dec 2019 13:26:08 GMT

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

←Older revision

Revision as of 13:26, 11 December 2019

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

OCA — Wed, 11 Dec 2019 13:26:06 GMT

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

New page

'''Unreleased structure'''

The entry 6lff is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]