6dwy - Revision history

OCA at 06:15, 11 October 2023

OCA — Wed, 11 Oct 2023 06:15:08 GMT

←Older revision		Revision as of 06:15, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6dwy' size='340' side='right'caption='[[6dwy]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6dwy' size='340' side='right'caption='[[6dwy]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dwy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~House_fly House fly~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6DWY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dwy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Musca_domestica Musca domestica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DWY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 3.2Å</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=6dwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwy OCA], [~~http~~://pdbe.org/6dwy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dwy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dwy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwy ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=6dwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwy OCA], [https://pdbe.org/6dwy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dwy RCSB], [https://www.ebi.ac.uk/pdbsum/6dwy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q25438_MUSDO Q25438_MUSDO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: House fly]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dyda, F~~]]	+	[[Category: Musca domestica]]
-	[[Category: ~~Hickman, A B~~]]	+	[[Category: Dyda F]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Hickman AB]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Transposase~~]]	+

OCA at 09:08, 11 November 2020

OCA — Wed, 11 Nov 2020 09:08:33 GMT

←Older revision		Revision as of 09:08, 11 November 2020
Line 1:		Line 1:

	==Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+==		==Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+==
-	<StructureSection load='6dwy' size='340' side='right' caption='[[6dwy]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='6dwy' size='340' side='right'caption='[[6dwy]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dwy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DWY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dwy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/House_fly House fly]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DWY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6dwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwy OCA], [http://pdbe.org/6dwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dwy RCSB], [http://www.ebi.ac.uk/pdbsum/6dwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwy 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=6dwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwy OCA], [http://pdbe.org/6dwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dwy RCSB], [http://www.ebi.ac.uk/pdbsum/6dwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Some DNA transposons relocate from one genomic location to another using a mechanism that involves generating double-strand breaks at their transposon ends by forming hairpins on flanking DNA. The same double-strand break mode is employed by the V(D)J recombinase at signal-end/coding-end junctions during the generation of antibody diversity. How flanking hairpins are formed during DNA transposition has remained elusive. Here, we describe several co-crystal structures of the Hermes transposase bound to DNA that mimics the reaction step immediately prior to hairpin formation. Our results reveal a large DNA conformational change between the initial cleavage step and subsequent hairpin formation that changes which strand is acted upon by a single active site. We observed that two factors affect the conformational change: the complement of divalent metal ions bound by the catalytically essential DDE residues, and the identity of the -2 flanking base pair. Our data also provides a mechanistic link between the efficiency of hairpin formation (an A:T basepair is favored at the -2 position) and Hermes' strong target site preference. Furthermore, we have established that the histidine residue within a conserved C/DxxH motif present in many transposase families interacts directly with the scissile phosphate, suggesting a crucial role in catalysis.
		+
		+	Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase.,Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F Nucleic Acids Res. 2018 Nov 2;46(19):10286-10301. doi: 10.1093/nar/gky838. PMID:30239795<ref>PMID:30239795</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dwy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transposase 3D structures\|Transposase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: House fly]]
		+	[[Category: Large Structures]]
	[[Category: Dyda, F]]		[[Category: Dyda, F]]
	[[Category: Hickman, A B]]		[[Category: Hickman, A B]]

OCA at 19:51, 19 September 2018

OCA — Wed, 19 Sep 2018 19:51:13 GMT

←Older revision		Revision as of 19:51, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6dwy is ON HOLD until Paper Publication~~	+	==Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+==
-		+	<StructureSection load='6dwy' size='340' side='right' caption='[[6dwy]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~Authors: Dyda, F., Hickman, A.B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dwy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DWY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DWY FirstGlance]. <br>
-	~~Description:~~ Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6dwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dwy OCA], [http://pdbe.org/6dwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dwy RCSB], [http://www.ebi.ac.uk/pdbsum/6dwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dwy ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Hickman~~, A.B]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Dyda, F]]		[[Category: Dyda, F]]
		+	[[Category: Hickman, A B]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Transposase]]

OCA at 05:26, 18 July 2018

OCA — Wed, 18 Jul 2018 05:26:57 GMT

←Older revision		Revision as of 05:26, 18 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Dyda, F., Hickman, A.B.		Authors: Dyda, F., Hickman, A.B.

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

OCA — Wed, 04 Jul 2018 05:49:13 GMT

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

←Older revision

Revision as of 05:49, 4 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dwy is ON HOLD Authors: Dyda, F., Hickman, A.B. Description: Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+ [[Category: Unrelea...

OCA — Wed, 04 Jul 2018 05:49:12 GMT

New page: '''Unreleased structure''' The entry 6dwy is ON HOLD Authors: Dyda, F., Hickman, A.B. Description: Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+ [[Category: Unrelea...

New page

'''Unreleased structure'''

The entry 6dwy is ON HOLD

Authors: Dyda, F., Hickman, A.B.

Description: Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+
[[Category: Unreleased Structures]]
[[Category: Hickman, A.B]]
[[Category: Dyda, F]]