4ncb - Revision history

OCA at 16:53, 20 September 2023

OCA — Wed, 20 Sep 2023 16:53:03 GMT

←Older revision		Revision as of 16:53, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ncb]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NCB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ncb]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NCB 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></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]] 2.189Å</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></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=4ncb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncb OCA], [https://pdbe.org/4ncb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ncb RCSB], [https://www.ebi.ac.uk/pdbsum/4ncb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncb 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=4ncb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncb OCA], [https://pdbe.org/4ncb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ncb RCSB], [https://www.ebi.ac.uk/pdbsum/4ncb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncb ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:21, 11 January 2023

OCA — Wed, 11 Jan 2023 08:21:57 GMT

←Older revision		Revision as of 08:21, 11 January 2023
Line 1:		Line 1:

	==Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+==		==Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+==
-	<StructureSection load='4ncb' size='340' side='right' caption='[[4ncb]], [[Resolution\|resolution]] 2.19Å' scene=''>	+	<StructureSection load='4ncb' size='340' side='right'caption='[[4ncb]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ncb]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NCB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ncb]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NCB 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>~~</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></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n41\|4n41]], [[4n47\|4n47]], [[4n76\|4n76]], [[4nca\|4nca]]</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=4ncb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncb OCA], [https://pdbe.org/4ncb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ncb RCSB], [https://www.ebi.ac.uk/pdbsum/4ncb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncb ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Argonaute, TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=4ncb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncb OCA], [~~http~~://pdbe.org/4ncb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ncb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ncb PDBsum]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q746M7_THET2 Q746M7_THET2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Argonaute\|Argonaute]]	+	*[[Argonaute 3D structures\|Argonaute 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Flavobacterium thermophilum yoshida and oshima 1971~~]]	+	[[Category: Large Structures]]
-	[[Category: Rao, Y]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Sheng, G]]	+	[[Category: Rao Y]]
-	[[Category: Wang, J]]	+	[[Category: Sheng G]]
-	[[Category: Wang, Y]]	+	[[Category: Wang J]]
-	[[Category: Zhao, H]]	+	[[Category: Wang Y]]
-	~~[[Category: Argonaute]]~~	+	[[Category: Zhao H]]
-	~~[[Category: Dna interference]]~~	+
-	~~[[Category: Nuclear protein-dna complex]]~~	+
-	~~[[Category: Piwi]]~~	+
-	~~[[Category: Rna interference~~]]	+

OCA at 08:01, 20 June 2016

OCA — Mon, 20 Jun 2016 08:01:51 GMT

←Older revision		Revision as of 08:01, 20 June 2016
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-	{{STRUCTURE_4ncb\| PDB=4ncb \| SCENE= }}
-	===Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+===
-	{{ABSTRACT_PUBMED_24374628}}

-	==~~About this~~ Structure==	+	==Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+==
-	[[4ncb]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA].	+	<StructureSection load='4ncb' size='340' side='right' caption='[[4ncb]], [[Resolution\|resolution]] 2.19Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ncb]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NCB 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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n41\|4n41]], [[4n47\|4n47]], [[4n76\|4n76]], [[4nca\|4nca]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Argonaute, TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=4ncb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncb OCA], [http://pdbe.org/4ncb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ncb RCSB], [http://www.ebi.ac.uk/pdbsum/4ncb PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5'-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 A have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg2+ cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand.

-	~~==Reference==~~	+	Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.,Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y Proc Natl Acad Sci U S A. 2013 Dec 27. PMID:24374628<ref>PMID:24374628</ref>
-	<ref ~~group="xtra"~~>PMID:~~024374628~~</ref><~~references group~~="~~xtra~~"/><references/>	+
-	[[Category: Rao, Y.]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Sheng, G.]]	+	</div>
-	[[Category: Wang, J.]]	+	<div class="pdbe-citations 4ncb" style="background-color:#fffaf0;"></div>
-	[[Category: Wang, Y.]]	+
-	[[Category: Zhao, H.]]	+	==See Also==
		+	*[[Argonaute\|Argonaute]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Rao, Y]]
		+	[[Category: Sheng, G]]
		+	[[Category: Wang, J]]
		+	[[Category: Wang, Y]]
		+	[[Category: Zhao, H]]
	[[Category: Argonaute]]		[[Category: Argonaute]]
	[[Category: Dna interference]]		[[Category: Dna interference]]

OCA at 08:13, 15 January 2014

OCA — Wed, 15 Jan 2014 08:13:10 GMT

←Older revision		Revision as of 08:13, 15 January 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4ncb\| PDB=4ncb \| SCENE= }}
		+	===Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+===
		+	{{ABSTRACT_PUBMED_24374628}}

-	~~The entry~~ 4ncb is ~~ON HOLD~~	+	==About this Structure==
		+	[[4ncb]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA].

-	~~Authors~~: Sheng, G.~~, Zhao, H.,~~ Wang, J.~~, Rao~~, Y., ~~Wang, Y~~.	+	==Reference==
-		+	<ref group="xtra">PMID:024374628</ref><references group="xtra"/><references/>
-	~~Description~~:	+	[[Category: Rao, Y.]]
		+	[[Category: Sheng, G.]]
		+	[[Category: Wang, J.]]
		+	[[Category: Wang, Y.]]
		+	[[Category: Zhao, H.]]
		+	[[Category: Argonaute]]
		+	[[Category: Dna interference]]
		+	[[Category: Nuclear protein-dna complex]]
		+	[[Category: Piwi]]
		+	[[Category: Rna interference]]

OCA at 09:22, 25 December 2013

OCA — Wed, 25 Dec 2013 09:22:32 GMT

←Older revision		Revision as of 09:22, 25 December 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ncb is ON HOLD ~~until sometime in the future~~	+	The entry 4ncb is ON HOLD

	Authors: Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y.		Authors: Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y.

-	Description: ~~DNA binding protein and DNA complex structrue~~	+	Description:

OCA at 12:56, 20 November 2013

OCA — Wed, 20 Nov 2013 12:56:58 GMT

←Older revision		Revision as of 12:56, 20 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ncb is ON HOLD	+	The entry 4ncb is ON HOLD until sometime in the future

	Authors: Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y.		Authors: Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y.

	Description: DNA binding protein and DNA complex structrue		Description: DNA binding protein and DNA complex structrue

OCA: Protected "4ncb" [edit=sysop:move=sysop]

OCA — Wed, 06 Nov 2013 07:08:33 GMT

Protected "4ncb" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:08, 6 November 2013

OCA: New page: '''Unreleased structure''' The entry 4ncb is ON HOLD Authors: Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y. Description: DNA binding protein and DNA complex structrue

OCA — Wed, 06 Nov 2013 07:08:32 GMT

New page: '''Unreleased structure''' The entry 4ncb is ON HOLD Authors: Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y. Description: DNA binding protein and DNA complex structrue

New page

'''Unreleased structure'''

The entry 4ncb is ON HOLD

Authors: Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y.

Description: DNA binding protein and DNA complex structrue