3tai - Revision history

OCA at 16:49, 6 July 2022

OCA — Wed, 06 Jul 2022 16:49:52 GMT

←Older revision		Revision as of 16:49, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of NurA==		==Crystal structure of NurA==
-	<StructureSection load='3tai' size='340' side='right' caption='[[3tai]], [[Resolution\|resolution]] 2.82Å' scene=''>	+	<StructureSection load='3tai' size='340' side='right'caption='[[3tai]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tai]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tai]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tal\|3tal]], [[3taz\|3taz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tal\|3tal]], [[3taz\|3taz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1168 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1168 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3tai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tai OCA], [~~http~~://pdbe.org/3tai PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tai RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tai PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tai ProSAT]</span></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=3tai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tai OCA], [https://pdbe.org/3tai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tai RCSB], [https://www.ebi.ac.uk/pdbsum/3tai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tai ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrfu]]		[[Category: Pyrfu]]
	[[Category: Chae, J]]		[[Category: Chae, J]]

OCA at 16:47, 5 August 2016

OCA — Fri, 05 Aug 2016 16:47:14 GMT

←Older revision		Revision as of 16:47, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of NurA==		==Crystal structure of NurA==
	<StructureSection load='3tai' size='340' side='right' caption='[[3tai]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='3tai' size='340' side='right' caption='[[3tai]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tai]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tai]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tal\|3tal]], [[3taz\|3taz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tal\|3tal]], [[3taz\|3taz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1168 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 ~~Pyrococcus furiosus DSM 3638~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1168 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3tai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tai RCSB], [http://www.ebi.ac.uk/pdbsum/3tai PDBsum]</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=3tai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tai OCA], [http://pdbe.org/3tai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tai RCSB], [http://www.ebi.ac.uk/pdbsum/3tai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tai ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3tai" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus furiosus dsm 3638~~]]	+	[[Category: Pyrfu]]
	[[Category: Chae, J]]		[[Category: Chae, J]]
	[[Category: Cho, Y]]		[[Category: Cho, Y]]

OCA at 07:34, 21 December 2014

OCA — Sun, 21 Dec 2014 07:34:02 GMT

←Older revision		Revision as of 07:34, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3tai\| PDB~~=3tai \| ~~SCENE~~= }}	+	==Crystal structure of NurA==
-	===~~Crystal~~ structure ~~of NurA~~===	+	<StructureSection load='3tai' size='340' side='right' caption='[[3tai]], [[Resolution\|resolution]] 2.82Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22064858}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tai]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TAI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tal\|3tal]], [[3taz\|3taz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1168 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638])</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=3tai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tai RCSB], [http://www.ebi.ac.uk/pdbsum/3tai PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf NurA) to provide the basis for its cleavage mechanism. Pf NurA forms a pyramid-shaped dimer containing a large central channel on one side, which becomes narrower towards the peak of the pyramid. The structure contains a PIWI domain with high similarity to argonaute, endoV nuclease and RNase H. The two active sites, each of which contains Mn(2)(+) ion(s) and dAMP, are at the corners of the elliptical channel near the flat face of the dimer. The 3' OH group of the ribose ring is directed toward the channel entrance, explaining the 5'-3' nuclease activity of Pf NurA. We provide a DNA binding and cleavage model for Pf NurA.

-	~~==About this Structure==~~	+	Crystal structure of the NurA-dAMP-Mn2+ complex.,Chae J, Kim YC, Cho Y Nucleic Acids Res. 2011 Nov 7. PMID:22064858<ref>PMID:22064858</ref>
-	~~[[3tai]] is a 2 chain~~ structure ~~with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:022064858</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Pyrococcus furiosus dsm 3638]]		[[Category: Pyrococcus furiosus dsm 3638]]
-	[[Category: Chae, J.]]	+	[[Category: Chae, J]]
-	[[Category: Cho, Y.]]	+	[[Category: Cho, Y]]
-	[[Category: Kim, Y C.]]	+	[[Category: Kim, Y C]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Recombination]]		[[Category: Recombination]]

OCA at 12:35, 3 July 2013

OCA — Wed, 03 Jul 2013 12:35:17 GMT

←Older revision		Revision as of 12:35, 3 July 2013
Line 1:		Line 1:
-	[[Image:3tai.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3tai", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3tai\| PDB=3tai \| SCENE= }}		{{STRUCTURE_3tai\| PDB=3tai \| SCENE= }}
-
	===Crystal structure of NurA===		===Crystal structure of NurA===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22064858}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22064858 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22064858}}		{{ABSTRACT_PUBMED_22064858}}

	==About this Structure==		==About this Structure==
-	[[3tai]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus~~ Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA].	+	[[3tai]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022064858</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022064858</ref><references group="xtra"/><references/>
-	[[Category: Pyrococcus furiosus]]	+	[[Category: Pyrococcus furiosus dsm 3638]]
	[[Category: Chae, J.]]		[[Category: Chae, J.]]
	[[Category: Cho, Y.]]		[[Category: Cho, Y.]]

OCA at 19:06, 23 November 2011

OCA — Wed, 23 Nov 2011 19:06:32 GMT

←Older revision		Revision as of 19:06, 23 November 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tai.jpg\|left\|200px]]

-	The ~~entry 3tai~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3tai", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3tai\| PDB=3tai \| SCENE= }}

-	~~Authors: Chae, J., Kim, Y.C., Cho, Y.~~	+	===Crystal structure of NurA===

-	~~Description~~: ~~Crystal~~ structure ~~of NurA~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22064858}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22064858 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22064858}}
		+
		+	==About this Structure==
		+	[[3tai]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAI OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022064858</ref><references group="xtra"/>
		+	[[Category: Pyrococcus furiosus]]
		+	[[Category: Chae, J.]]
		+	[[Category: Cho, Y.]]
		+	[[Category: Kim, Y C.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Recombination]]

OCA at 11:46, 16 November 2011

OCA — Wed, 16 Nov 2011 11:46:16 GMT

←Older revision		Revision as of 11:46, 16 November 2011
Line 5:		Line 5:
	Authors: Chae, J., Kim, Y.C., Cho, Y.		Authors: Chae, J., Kim, Y.C., Cho, Y.

-	Description: ~~DNA repair protein1~~	+	Description: Crystal structure of NurA

OCA at 06:02, 14 September 2011

OCA — Wed, 14 Sep 2011 06:02:44 GMT

←Older revision		Revision as of 06:02, 14 September 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tai is ON HOLD	+	The entry 3tai is ON HOLD until Paper Publication

	Authors: Chae, J., Kim, Y.C., Cho, Y.		Authors: Chae, J., Kim, Y.C., Cho, Y.

	Description: DNA repair protein1		Description: DNA repair protein1

OCA: Protected "3tai" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2011 05:39:18 GMT

Protected "3tai" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:39, 10 August 2011

OCA: New page: '''Unreleased structure''' The entry 3tai is ON HOLD Authors: Chae, J., Kim, Y.C., Cho, Y. Description: DNA repair protein1

OCA — Wed, 10 Aug 2011 05:39:15 GMT

New page: '''Unreleased structure''' The entry 3tai is ON HOLD Authors: Chae, J., Kim, Y.C., Cho, Y. Description: DNA repair protein1

New page

'''Unreleased structure'''

The entry 3tai is ON HOLD

Authors: Chae, J., Kim, Y.C., Cho, Y.

Description: DNA repair protein1