5wvy - Revision history

OCA at 07:49, 22 November 2023

OCA — Wed, 22 Nov 2023 07:49:16 GMT

←Older revision		Revision as of 07:49, 22 November 2023
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	==The crystal structure of Cren7 mutant L28V in complex with dsDNA==		==The crystal structure of Cren7 mutant L28V in complex with dsDNA==
-	<StructureSection load='5wvy' size='340' side='right' caption='[[5wvy]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5wvy' size='340' side='right'caption='[[5wvy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wvy]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sulso Sulso~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wvy]] 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=5WVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WVY FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5wvw\|5wvw]], [[5wvz\|5wvz]], [[5wwc\|5wwc]]</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]] 2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">creN7, SSO6901 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=273057 SULSO])~~</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=5wvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvy OCA], [https://pdbe.org/5wvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wvy RCSB], [https://www.ebi.ac.uk/pdbsum/5wvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvy 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=5wvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvy OCA], [~~http~~://pdbe.org/5wvy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wvy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wvy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvy 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sulso~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Chen, Y Y~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: ~~Dong, Y H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Gong, Y~~]]	+	[[Category: Chen YY]]
-	[[Category: ~~Huang, L~~]]	+	[[Category: Dong YH]]
-	[[Category: ~~Wang, L~~]]	+	[[Category: Gong Y]]
-	[[Category: ~~Zhang, Z F~~]]	+	[[Category: Huang L]]
-	[[Category: ~~Zhao, M H~~]]	+	[[Category: Wang L]]
-	[[Category: ~~Beta-sheet~~]]	+	[[Category: Zhang ZF]]
-	[[Category: ~~Crenarchaeal chromatin protein]]~~	+	[[Category: Zhao MH]]
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Dna binding protein-dna complex~~]]	+

OCA at 14:45, 6 November 2017

OCA — Mon, 06 Nov 2017 14:45:16 GMT

←Older revision		Revision as of 14:45, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5wvy' size='340' side='right' caption='[[5wvy]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5wvy' size='340' side='right' caption='[[5wvy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wvy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wvy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WVY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wvw\|5wvw]], [[5wvz\|5wvz]], [[5wwc\|5wwc]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wvw\|5wvw]], [[5wvz\|5wvz]], [[5wwc\|5wwc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">creN7, SSO6901 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=5wvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvy OCA], [http://pdbe.org/5wvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wvy RCSB], [http://www.ebi.ac.uk/pdbsum/5wvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvy 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=5wvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvy OCA], [http://pdbe.org/5wvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wvy RCSB], [http://www.ebi.ac.uk/pdbsum/5wvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvy ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Sulso]]
	[[Category: Chen, Y Y]]		[[Category: Chen, Y Y]]
	[[Category: Dong, Y H]]		[[Category: Dong, Y H]]

OCA at 13:49, 27 April 2017

OCA — Thu, 27 Apr 2017 13:49:43 GMT

←Older revision		Revision as of 13:49, 27 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5wvy is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==The crystal structure of Cren7 mutant L28V in complex with dsDNA==
		+	<StructureSection load='5wvy' size='340' side='right' caption='[[5wvy]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wvy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WVY FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wvw\|5wvw]], [[5wvz\|5wvz]], [[5wwc\|5wwc]]</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=5wvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wvy OCA], [http://pdbe.org/5wvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wvy RCSB], [http://www.ebi.ac.uk/pdbsum/5wvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wvy 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 ==
		+	Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologues, intercalates into the kink DNA step. In this study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e., L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain. Structural analysis shows that L28A induces a kink (~43o), nearly as sharp as that produced by wild-type Cren7 (~48o), in the bound DNA despite the lack of side chain intercalation. L28F inserts a large hydrophobic side chain deep into the DNA step, but introduces a smaller kink (~39o) than that formed by the wild-type protein (~50o). Mutation of Leu28 into methionine yields two protein conformers differing in loop beta3-beta4 orientation as well as DNA binding surface and DNA geometry in the protein-DNA structure. Our results indicate that side chain intercalation is not directly responsible for DNA kinking or bending by Cren7, but plays a critical role in the stabilization of the Cren7-DNA complex. In addition, the flexibility of loop beta3-beta4 in Cren7, as revealed in the crystal structure of L28M-DNA, may serve a role in the modulation of chromosomal organization and function in the cell.

-	~~Authors: Zhang~~, Z~~.F.~~, Zhao, M~~.H.~~, Wang, L., Chen, Y~~.Y.~~, Dong, Y~~.H.~~, Gong, Y., Huang, L.	+	Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA.,Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y, Huang L Biochem J. 2017 Apr 4. pii: BCJ20170036. doi: 10.1042/BCJ20170036. PMID:28377493<ref>PMID:28377493</ref>

-	~~Description: The crystal structure~~ of ~~Cren7 mutant L28V in complex with dsDNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5wvy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, Y Y]]
		+	[[Category: Dong, Y H]]
		+	[[Category: Gong, Y]]
	[[Category: Huang, L]]		[[Category: Huang, L]]
-	[[Category: Chen, Y.Y]]
-	[[Category: Dong, Y.H]]
	[[Category: Wang, L]]		[[Category: Wang, L]]
-	[[Category: Zhao, M.H]]	+	[[Category: Zhang, Z F]]
-	[[Category: ~~Zhang, Z.F~~]]	+	[[Category: Zhao, M H]]
-	[[Category: ~~Gong, Y~~]]	+	[[Category: Beta-sheet]]
		+	[[Category: Crenarchaeal chromatin protein]]
		+	[[Category: Dna binding]]
		+	[[Category: Dna binding protein-dna complex]]

OCA at 19:54, 15 March 2017

OCA — Wed, 15 Mar 2017 19:54:56 GMT

←Older revision		Revision as of 19:54, 15 March 2017
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	Description: The crystal structure of Cren7 mutant L28V in complex with dsDNA		Description: The crystal structure of Cren7 mutant L28V in complex with dsDNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Wang, L]]
-	[[Category: Zhao, M.H]]
	[[Category: Huang, L]]		[[Category: Huang, L]]
	[[Category: Chen, Y.Y]]		[[Category: Chen, Y.Y]]
	[[Category: Dong, Y.H]]		[[Category: Dong, Y.H]]
		+	[[Category: Wang, L]]
		+	[[Category: Zhao, M.H]]
	[[Category: Zhang, Z.F]]		[[Category: Zhang, Z.F]]
	[[Category: Gong, Y]]		[[Category: Gong, Y]]

OCA at 15:15, 18 January 2017

OCA — Wed, 18 Jan 2017 15:15:20 GMT

←Older revision		Revision as of 15:15, 18 January 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zhang, Z.F., Zhao, M.H., Wang, L., Chen, Y.Y., Dong, Y.H., Gong, Y., Huang, L.		Authors: Zhang, Z.F., Zhao, M.H., Wang, L., Chen, Y.Y., Dong, Y.H., Gong, Y., Huang, L.

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

OCA — Wed, 04 Jan 2017 15:57:24 GMT

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

←Older revision

Revision as of 15:57, 4 January 2017

OCA: New page: '''Unreleased structure''' The entry 5wvy is ON HOLD Authors: Zhang, Z.F., Zhao, M.H., Wang, L., Chen, Y.Y., Dong, Y.H., Gong, Y., Huang, L. Description: The crystal structure of Cren7...

OCA — Wed, 04 Jan 2017 15:57:23 GMT

New page: '''Unreleased structure''' The entry 5wvy is ON HOLD Authors: Zhang, Z.F., Zhao, M.H., Wang, L., Chen, Y.Y., Dong, Y.H., Gong, Y., Huang, L. Description: The crystal structure of Cren7...

New page

'''Unreleased structure'''

The entry 5wvy is ON HOLD

Authors: Zhang, Z.F., Zhao, M.H., Wang, L., Chen, Y.Y., Dong, Y.H., Gong, Y., Huang, L.

Description: The crystal structure of Cren7 mutant L28V in complex with dsDNA
[[Category: Unreleased Structures]]
[[Category: Wang, L]]
[[Category: Zhao, M.H]]
[[Category: Huang, L]]
[[Category: Chen, Y.Y]]
[[Category: Dong, Y.H]]
[[Category: Zhang, Z.F]]
[[Category: Gong, Y]]