5k17 - Revision history

OCA at 19:17, 20 September 2023

OCA — Wed, 20 Sep 2023 19:17:42 GMT

←Older revision		Revision as of 19:17, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5k17' size='340' side='right'caption='[[5k17]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5k17' size='340' side='right'caption='[[5k17]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k17]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sacs2 Sacs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K17 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K17 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k17]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2] 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=5K17 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K17 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5k07\|5k07]]</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]] 2.1Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">creN7 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=273057 SACS2])~~</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=5k17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k17 OCA], [https://pdbe.org/5k17 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k17 RCSB], [https://www.ebi.ac.uk/pdbsum/5k17 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k17 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=5k17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k17 OCA], [~~http~~://pdbe.org/5k17 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k17 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k17 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k17 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~CREN7_SULSO CREN7_SULSO]~~] A highly abundant probable chromatin protein, it binds double-strand DNA without sequence specificity; there is approximately 1 Cren7 molecule for 12 bp of DNA. Constrains negative DNA supercoils, increases DNA stability against thermal denaturation. Binding does not require protein methylation. Binds single-strand DNA weakly.<ref>PMID:18096617</ref>	+	[https://www.uniprot.org/uniprot/CREN7_SACS2 CREN7_SACS2] A highly abundant probable chromatin protein, it binds double-strand DNA without sequence specificity; there is approximately 1 Cren7 molecule for 12 bp of DNA. Constrains negative DNA supercoils, increases DNA stability against thermal denaturation. Binding does not require protein methylation. Binds single-strand DNA weakly.<ref>PMID:18096617</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sacs2~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: ~~Gong, Y~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Zhang, Z F~~]]	+	[[Category: Gong Y]]
-	[[Category: ~~Beta-sheet]]~~	+	[[Category: Zhang ZF]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Methylation]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 09:13, 25 June 2020

OCA — Thu, 25 Jun 2020 09:13:41 GMT

←Older revision		Revision as of 09:13, 25 June 2020
Line 1:		Line 1:

	==Crystal structure of CREN7-DSDNA (GTGATCGC) complex==		==Crystal structure of CREN7-DSDNA (GTGATCGC) complex==
-	<StructureSection load='5k17' size='340' side='right' caption='[[5k17]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5k17' size='340' side='right'caption='[[5k17]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k17]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K17 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K17 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k17]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sacs2 Sacs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K17 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K17 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k07\|5k07]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k07\|5k07]]</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=5k17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k17 OCA], [http://pdbe.org/5k17 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k17 RCSB], [http://www.ebi.ac.uk/pdbsum/5k17 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k17 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">creN7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SACS2])</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=5k17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k17 OCA], [http://pdbe.org/5k17 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k17 RCSB], [http://www.ebi.ac.uk/pdbsum/5k17 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k17 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sacs2]]
	[[Category: Gong, Y]]		[[Category: Gong, Y]]
	[[Category: Zhang, Z F]]		[[Category: Zhang, Z F]]

OCA at 13:39, 24 May 2017

OCA — Wed, 24 May 2017 13:39:22 GMT

←Older revision		Revision as of 13:39, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k17 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of CREN7-DSDNA (GTGATCGC) complex==
		+	<StructureSection load='5k17' size='340' side='right' caption='[[5k17]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k17]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K17 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K17 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k07\|5k07]]</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=5k17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k17 OCA], [http://pdbe.org/5k17 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k17 RCSB], [http://www.ebi.ac.uk/pdbsum/5k17 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k17 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CREN7_SULSO CREN7_SULSO]] A highly abundant probable chromatin protein, it binds double-strand DNA without sequence specificity; there is approximately 1 Cren7 molecule for 12 bp of DNA. Constrains negative DNA supercoils, increases DNA stability against thermal denaturation. Binding does not require protein methylation. Binds single-strand DNA weakly.<ref>PMID:18096617</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	T:G base pair arising from spontaneous deamination of 5mC or polymerase errors is a great challenge for DNA repair of hyperthermophilic archaea, especially Crenarchaea. Most strains in this phylum lack the protein homologues responsible for the recognition of the mismatch in the DNA repair pathways. To investigate whether Cren7, a highly conserved chromatin protein in Crenarchaea, serves a role in the repair of T:G mispairs, the crystal structures of Cren7-GTAATTGC and Cren7-GTGATCGC complexes were solved at 2.0 A and 2.1 A. In our structures, binding of Cren7 to the AT-rich DNA duplex (GTAATTGC) induces opening of T2:G15 but not T10:G7 base pair. By contrast, both T:G mispairs in the GC-rich DNA duplex (GTGATCGC) retain the classic wobble type. Structural analysis also showed DNA helical changes of GTAATTGC, especially in the steps around the open T:G base pair, as compared to GTGATCGC or the matched DNAs. Surface plasmon resonance assays revealed a 4-fold lower binding affinity of Cren7 for GTAATTGC than that for GTGATCGC, which was dominantly contributed by the decrease of association rate. These results suggested that binding of Cren7 to DNA leads to T:G mispair opening in a sequence dependent manner, and therefore propose the potential roles of Cren7 in DNA repair.

-	~~Authors~~: ~~Zhang~~, ~~Z.F~~., ~~Gong~~, Y.	+	Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea.,Tian L, Zhang Z, Wang H, Zhao M, Dong Y, Gong Y PLoS One. 2016 Sep 29;11(9):e0163361. doi: 10.1371/journal.pone.0163361., eCollection 2016. PMID:27685992<ref>PMID:27685992</ref>

-	~~Description: Crystal structure~~ of ~~CREN7-DSDNA (GTGATCGC) complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Zhang, Z.F]]~~	+	<div class="pdbe-citations 5k17" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gong, Y]]		[[Category: Gong, Y]]
		+	[[Category: Zhang, Z F]]
		+	[[Category: Beta-sheet]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna-binding]]
		+	[[Category: Methylation]]
		+	[[Category: Protein-dna complex]]

OCA: Protected "5k17" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:10:39 GMT

Protected "5k17" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:10, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k17 is ON HOLD until Paper Publication Authors: Zhang, Z.F., Gong, Y. Description: Crystal structure of CREN7-DSDNA (GTGATCGC) complex [[Category:...

OCA — Wed, 01 Jun 2016 14:10:38 GMT

New page: '''Unreleased structure''' The entry 5k17 is ON HOLD until Paper Publication Authors: Zhang, Z.F., Gong, Y. Description: Crystal structure of CREN7-DSDNA (GTGATCGC) complex [[Category:...

New page

'''Unreleased structure'''

The entry 5k17 is ON HOLD until Paper Publication

Authors: Zhang, Z.F., Gong, Y.

Description: Crystal structure of CREN7-DSDNA (GTGATCGC) complex
[[Category: Unreleased Structures]]
[[Category: Zhang, Z.F]]
[[Category: Gong, Y]]