6pr5 - Revision history

OCA at 09:27, 20 March 2024

OCA — Wed, 20 Mar 2024 09:27:08 GMT

←Older revision		Revision as of 09:27, 20 March 2024
Line 3:		Line 3:
	<SX load='6pr5' size='340' side='right' viewer='molstar' caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6pr5' size='340' side='right' viewer='molstar' caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Corn_earworm_moth Corn earworm moth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicoverpa_zea Helicoverpa zea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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">Electron Microscopy, [[Resolution\|Resolution]] 3.3Å</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=6pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pr5 OCA], [~~http~~://pdbe.org/6pr5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pr5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pr5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pr5 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=6pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pr5 OCA], [https://pdbe.org/6pr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pr5 RCSB], [https://www.ebi.ac.uk/pdbsum/6pr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pr5 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/B0F0C5_HELZE B0F0C5_HELZE]
-	Transposons have had a pivotal role in genome evolution(1) and are believed to be the evolutionary progenitors of the RAG1-RAG2 recombinase(2), an essential component of the adaptive immune system in jawed vertebrates(3). Here we report one crystal structure and five cryo-electron microscopy structures of Transib(4,5), a RAG1-like transposase from Helicoverpa zea, that capture the entire transposition process from the apo enzyme to the terminal strand transfer complex with transposon ends covalently joined to target DNA, at resolutions of 3.0-4.6 A. These structures reveal a butterfly-shaped complex that undergoes two cycles of marked conformational changes in which the 'wings' of the transposase unfurl to bind substrate DNA, close to execute cleavage, open to release the flanking DNA and close again to capture and attack target DNA. Transib possesses unique structural elements that compensate for the absence of a RAG2 partner, including a loop that interacts with the transposition target site and an accordion-like C-terminal tail that elongates and contracts to help to control the opening and closing of the enzyme and assembly of the active site. Our findings reveal the detailed reaction pathway of a eukaryotic cut-and-paste transposase and illuminate some of the earliest steps in the evolution of the RAG recombinase.	+
-		+
-	~~Structures of a RAG-like transposase during cut-and-paste transposition.,Liu C, Yang Y, Schatz DG Nature. 2019 Nov;575(7783)~~:~~540-544. doi: 10.1038~~/~~s41586-019-1753-7. Epub 2019 Nov, 13. PMID:31723264<ref>PMID:31723264<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6pr5" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Transposase 3D structures\|Transposase 3D structures]]		*[[Transposase 3D structures\|Transposase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Corn earworm moth~~]]	+	[[Category: Helicoverpa zea]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liu, C]]	+	[[Category: Liu C]]
-	[[Category: Schatz~~, D G~~]]	+	[[Category: Schatz DG]]
-	[[Category: Yang, Y]]	+	[[Category: Yang Y]]
-	~~[[Category: Dde family enzyme]]~~	+
-	~~[[Category: Rag-like transposase]]~~	+
-	~~[[Category: Recombination]]~~	+
-	~~[[Category: Recombination-dna complex]]~~	+
-	~~[[Category: Strand transfer]]~~	+
-	~~[[Category: Transib~~]]	+

OCA at 04:34, 11 April 2020

OCA — Sat, 11 Apr 2020 04:34:56 GMT

←Older revision		Revision as of 04:34, 11 April 2020
Line 3:		Line 3:
	<SX load='6pr5' size='340' side='right' viewer='molstar' caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6pr5' size='340' side='right' viewer='molstar' caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Corn_earworm_moth Corn earworm moth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Corn_earworm_moth Corn earworm moth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=6pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pr5 OCA], [http://pdbe.org/6pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/6pr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pr5 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=6pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pr5 OCA], [http://pdbe.org/6pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/6pr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pr5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:26, 6 March 2020

OCA — Fri, 06 Mar 2020 23:26:20 GMT

←Older revision		Revision as of 23:26, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of HzTransib strand transfer complex (STC)==		==Cryo-EM structure of HzTransib strand transfer complex (STC)==
-	<~~StructureSection~~ load='6pr5' size='340' side='right'caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<SX load='6pr5' size='340' side='right' viewer='molstar' caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Corn_earworm_moth Corn earworm moth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Corn_earworm_moth Corn earworm moth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 6pr5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6pr5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transposase 3D structures\|Transposase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Corn earworm moth]]		[[Category: Corn earworm moth]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 09:20, 27 November 2019

OCA — Wed, 27 Nov 2019 09:20:17 GMT

←Older revision		Revision as of 09:20, 27 November 2019
Line 3:		Line 3:
	<StructureSection load='6pr5' size='340' side='right'caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6pr5' size='340' side='right'caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Corn_earworm_moth Corn earworm moth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=MG:MAGNESIUM+ION'>MG</scene>, <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=6pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pr5 OCA], [http://pdbe.org/6pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/6pr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pr5 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=6pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pr5 OCA], [http://pdbe.org/6pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/6pr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pr5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transposons have had a pivotal role in genome evolution(1) and are believed to be the evolutionary progenitors of the RAG1-RAG2 recombinase(2), an essential component of the adaptive immune system in jawed vertebrates(3). Here we report one crystal structure and five cryo-electron microscopy structures of Transib(4,5), a RAG1-like transposase from Helicoverpa zea, that capture the entire transposition process from the apo enzyme to the terminal strand transfer complex with transposon ends covalently joined to target DNA, at resolutions of 3.0-4.6 A. These structures reveal a butterfly-shaped complex that undergoes two cycles of marked conformational changes in which the 'wings' of the transposase unfurl to bind substrate DNA, close to execute cleavage, open to release the flanking DNA and close again to capture and attack target DNA. Transib possesses unique structural elements that compensate for the absence of a RAG2 partner, including a loop that interacts with the transposition target site and an accordion-like C-terminal tail that elongates and contracts to help to control the opening and closing of the enzyme and assembly of the active site. Our findings reveal the detailed reaction pathway of a eukaryotic cut-and-paste transposase and illuminate some of the earliest steps in the evolution of the RAG recombinase.
		+
		+	Structures of a RAG-like transposase during cut-and-paste transposition.,Liu C, Yang Y, Schatz DG Nature. 2019 Nov;575(7783):540-544. doi: 10.1038/s41586-019-1753-7. Epub 2019 Nov, 13. PMID:31723264<ref>PMID:31723264</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pr5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Corn earworm moth]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Liu, C]]		[[Category: Liu, C]]

OCA at 05:22, 10 October 2019

OCA — Thu, 10 Oct 2019 05:22:57 GMT

←Older revision		Revision as of 05:22, 10 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pr5 ~~is ON HOLD until Paper Publication~~	+	==Cryo-EM structure of HzTransib strand transfer complex (STC)==
-		+	<StructureSection load='6pr5' size='340' side='right'caption='[[6pr5]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6pr5]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PR5 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6pr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pr5 OCA], [http://pdbe.org/6pr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pr5 RCSB], [http://www.ebi.ac.uk/pdbsum/6pr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pr5 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Liu, C]]
		+	[[Category: Schatz, D G]]
		+	[[Category: Yang, Y]]
		+	[[Category: Dde family enzyme]]
		+	[[Category: Rag-like transposase]]
		+	[[Category: Recombination]]
		+	[[Category: Recombination-dna complex]]
		+	[[Category: Strand transfer]]
		+	[[Category: Transib]]

OCA at 04:42, 31 July 2019

OCA — Wed, 31 Jul 2019 04:42:54 GMT

←Older revision		Revision as of 04:42, 31 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pr5 is ON HOLD	+	The entry 6pr5 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6pr5" [edit=sysop:move=sysop]

OCA — Wed, 17 Jul 2019 09:09:22 GMT

Protected "6pr5" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:09, 17 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pr5 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 Jul 2019 09:09:20 GMT

New page: '''Unreleased structure''' The entry 6pr5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pr5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]