6dbl - Revision history

OCA at 00:00, 11 April 2020

2020-04-11T00:00:12Z

←Older revision		Revision as of 00:00, 11 April 2020
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	<SX load='6dbl' size='340' side='right' viewer='molstar' caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>		<SX load='6dbl' size='340' side='right' viewer='molstar' caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DBL 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>, <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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dbi\|6dbi]], [[6dbj\|6dbj]], [[6dbo\|6dbo]], [[6dbq\|6dbq]], [[6dbr\|6dbr]], [[6dbu\|6dbu]], [[6dbv\|6dbv]], [[6dbw\|6dbw]], [[6dbx\|6dbx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dbi\|6dbi]], [[6dbj\|6dbj]], [[6dbo\|6dbo]], [[6dbq\|6dbq]], [[6dbr\|6dbr]], [[6dbu\|6dbu]], [[6dbv\|6dbv]], [[6dbw\|6dbw]], [[6dbx\|6dbx]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rag1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), rag2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rag1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), rag2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </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=6dbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbl OCA], [http://pdbe.org/6dbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbl RCSB], [http://www.ebi.ac.uk/pdbsum/6dbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbl 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=6dbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbl OCA], [http://pdbe.org/6dbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbl RCSB], [http://www.ebi.ac.uk/pdbsum/6dbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:52, 6 March 2020

2020-03-06T20:52:35Z

←Older revision		Revision as of 20:52, 6 March 2020
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	==Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs==		==Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs==
-	<~~StructureSection~~ load='6dbl' size='340' side='right'caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>	+	<SX load='6dbl' size='340' side='right' viewer='molstar' caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBL FirstGlance]. <br>
Line 27:		Line 27:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Brachidanio rerio]]		[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 10:03, 18 December 2019

2019-12-18T10:03:55Z

←Older revision		Revision as of 10:03, 18 December 2019
Line 1:		Line 1:

	==Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs==		==Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs==
-	<StructureSection load='6dbl' size='340' side='right' caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>	+	<StructureSection load='6dbl' size='340' side='right'caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBL FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6dbl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dbl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Recombination-activating gene 3D structures\|Recombination-activating gene 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Brachidanio rerio]]		[[Category: Brachidanio rerio]]
		+	[[Category: Large Structures]]
	[[Category: RING-type E3 ubiquitin transferase]]		[[Category: RING-type E3 ubiquitin transferase]]
	[[Category: Liao, M]]		[[Category: Liao, M]]

OCA at 16:38, 15 August 2018

2018-08-15T16:38:37Z

←Older revision		Revision as of 16:38, 15 August 2018
Line 3:		Line 3:
	<StructureSection load='6dbl' size='340' side='right' caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>		<StructureSection load='6dbl' size='340' side='right' caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBL 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>, <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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dbi\|6dbi]], [[6dbj\|6dbj]], [[6dbo\|6dbo]], [[6dbq\|6dbq]], [[6dbr\|6dbr]], [[6dbu\|6dbu]], [[6dbv\|6dbv]], [[6dbw\|6dbw]], [[6dbx\|6dbx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dbi\|6dbi]], [[6dbj\|6dbj]], [[6dbo\|6dbo]], [[6dbq\|6dbq]], [[6dbr\|6dbr]], [[6dbu\|6dbu]], [[6dbv\|6dbv]], [[6dbw\|6dbw]], [[6dbx\|6dbx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rag1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), rag2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </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=6dbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbl OCA], [http://pdbe.org/6dbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbl RCSB], [http://www.ebi.ac.uk/pdbsum/6dbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbl 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=6dbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbl OCA], [http://pdbe.org/6dbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbl RCSB], [http://www.ebi.ac.uk/pdbsum/6dbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbl ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.		[[http://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The mechanism for initiating DNA cleavage by DDE-family enzymes, including the RAG endonuclease, which initiates V(D)J recombination, is not well understood. Here we report six cryo-EM structures of zebrafish RAG in complex with one or two intact recombination signal sequences (RSSs), at up to 3.9-A resolution. Unexpectedly, these structures reveal DNA melting at the heptamer of the RSSs, thus resulting in a corkscrew-like rotation of coding-flank DNA and the positioning of the scissile phosphate in the active site. Substrate binding is associated with dimer opening and a piston-like movement in RAG1, first outward to accommodate unmelted DNA and then inward to wedge melted DNA. These precleavage complexes show limited base-specific contacts of RAG at the conserved terminal CAC/GTG sequence of the heptamer, thus suggesting conservation based on a propensity to unwind. CA and TG overwhelmingly dominate terminal sequences in transposons and retrotransposons, thereby implicating a universal mechanism for DNA melting during the initiation of retroviral integration and DNA transposition.
		+
		+	DNA melting initiates the RAG catalytic pathway.,Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H Nat Struct Mol Biol. 2018 Aug;25(8):732-742. doi: 10.1038/s41594-018-0098-5. Epub, 2018 Jul 30. PMID:30061602<ref>PMID:30061602</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dbl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: RING-type E3 ubiquitin transferase]]		[[Category: RING-type E3 ubiquitin transferase]]
	[[Category: Liao, M]]		[[Category: Liao, M]]

OCA at 18:48, 1 August 2018

2018-08-01T18:48:56Z

←Older revision		Revision as of 18:48, 1 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dbl is ~~ON HOLD until Paper Publication~~	+	==Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs==
-		+	<StructureSection load='6dbl' size='340' side='right' caption='[[6dbl]], [[Resolution\|resolution]] 5.00Å' scene=''>
-	~~Authors~~: Wu, H., ~~Liao~~, M., Ru, H., Mi, W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dbl]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBL FirstGlance]. <br>
-	~~Description~~: ~~Cryo-EM structure of RAG~~ in ~~complex with 12~~-~~RSS~~ and 23-~~RSS substrate DNAs~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dbi\|6dbi]], [[6dbj\|6dbj]], [[6dbo\|6dbo]], [[6dbq\|6dbq]], [[6dbr\|6dbr]], [[6dbu\|6dbu]], [[6dbv\|6dbv]], [[6dbw\|6dbw]], [[6dbx\|6dbx]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </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=6dbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbl OCA], [http://pdbe.org/6dbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbl RCSB], [http://www.ebi.ac.uk/pdbsum/6dbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RING-type E3 ubiquitin transferase]]
		+	[[Category: Liao, M]]
	[[Category: Mi, W]]		[[Category: Mi, W]]
-	[[Category: Liao, M]]
	[[Category: Ru, H]]		[[Category: Ru, H]]
	[[Category: Wu, H]]		[[Category: Wu, H]]
		+	[[Category: Melted dna]]
		+	[[Category: Pre-cleavage complex]]
		+	[[Category: Rag complex]]
		+	[[Category: Recombination-dna complex]]

OCA at 04:04, 16 May 2018

2018-05-16T04:04:18Z

←Older revision		Revision as of 04:04, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Wu, H., Liao, M., Ru, H., Mi, W.		Authors: Wu, H., Liao, M., Ru, H., Mi, W.

-	Description: RAG complex with ~~12Nick~~ and ~~23Nick~~ DNAs	+	Description: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Mi, W]]		[[Category: Mi, W]]

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

2018-05-09T04:58:32Z

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

←Older revision

Revision as of 04:58, 9 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dbl is ON HOLD Authors: Wu, H., Liao, M., Ru, H., Mi, W. Description: RAG complex with 12Nick and 23Nick DNAs Category: Unreleased Structures ...

2018-05-09T04:58:30Z

New page: '''Unreleased structure''' The entry 6dbl is ON HOLD Authors: Wu, H., Liao, M., Ru, H., Mi, W. Description: RAG complex with 12Nick and 23Nick DNAs Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 6dbl is ON HOLD

Authors: Wu, H., Liao, M., Ru, H., Mi, W.

Description: RAG complex with 12Nick and 23Nick DNAs
[[Category: Unreleased Structures]]
[[Category: Mi, W]]
[[Category: Liao, M]]
[[Category: Ru, H]]
[[Category: Wu, H]]