3dlh - Revision history

OCA at 09:41, 21 February 2024

OCA — Wed, 21 Feb 2024 09:41:54 GMT

←Older revision		Revision as of 09:41, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3dlh' size='340' side='right'caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3dlh' size='340' side='right'caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet2 Thet2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DLH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DLH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dlb\|3dlb]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])~~</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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [https://pdbe.org/3dlh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [https://www.ebi.ac.uk/pdbsum/3dlh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dlh 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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [https://pdbe.org/3dlh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [https://www.ebi.ac.uk/pdbsum/3dlh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dlh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q746M7_THET2 Q746M7_THET2]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dlh ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dlh ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.
-
-	Structure of the guide-strand-containing argonaute silencing complex.,Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ Nature. 2008 Nov 13;456(7219):209-13. Epub 2008 Aug 27. PMID:18754009<ref>PMID:18754009</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3dlh" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Argonaute 3D structures\|Argonaute 3D structures]]		*[[Argonaute 3D structures\|Argonaute 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet2~~]]	+	[[Category: Thermus thermophilus HB27]]
-	[[Category: Patel~~, D J~~]]	+	[[Category: Patel DJ]]
-	[[Category: Sheng, G]]	+	[[Category: Sheng G]]
-	[[Category: Wang, Y]]	+	[[Category: Wang Y]]
-	~~[[Category: Argonaute]]~~	+
-	~~[[Category: Nucleic acid binding protein-dna complex]]~~	+
-	~~[[Category: Plasmid]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 08:01, 9 February 2022

OCA — Wed, 09 Feb 2022 08:01:49 GMT

←Older revision		Revision as of 08:01, 9 February 2022
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	==Crystal structure of the guide-strand-containing Argonaute protein silencing complex==		==Crystal structure of the guide-strand-containing Argonaute protein silencing complex==
-	<StructureSection load='3dlh' size='340' side='right' caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='3dlh' size='340' side='right'caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DLH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DLH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlb\|3dlb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dlb\|3dlb]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [~~http~~://pdbe.org/3dlh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dlh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dlh 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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [https://pdbe.org/3dlh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [https://www.ebi.ac.uk/pdbsum/3dlh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dlh ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Argonaute\|Argonaute]]	+	*[[Argonaute 3D structures\|Argonaute 3D structures]]
-	*[[RNA Interference\|RNA Interference]]	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet2]]		[[Category: Thet2]]
	[[Category: Patel, D J]]		[[Category: Patel, D J]]

OCA at 09:36, 14 November 2018

OCA — Wed, 14 Nov 2018 09:36:59 GMT

←Older revision		Revision as of 09:36, 14 November 2018
Line 1:		Line 1:
		+
	==Crystal structure of the guide-strand-containing Argonaute protein silencing complex==		==Crystal structure of the guide-strand-containing Argonaute protein silencing complex==
	<StructureSection load='3dlh' size='340' side='right' caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3dlh' size='340' side='right' caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlb\|3dlb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlb\|3dlb]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [http://pdbe.org/3dlh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [http://www.ebi.ac.uk/pdbsum/3dlh 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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [http://pdbe.org/3dlh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [http://www.ebi.ac.uk/pdbsum/3dlh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dlh ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dlh_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dlh_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 41:		Line 42:
	[[Category: Argonaute]]		[[Category: Argonaute]]
	[[Category: Nucleic acid binding protein-dna complex]]		[[Category: Nucleic acid binding protein-dna complex]]
		+	[[Category: Plasmid]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

OCA at 01:34, 10 February 2016

OCA — Wed, 10 Feb 2016 01:34:46 GMT

←Older revision		Revision as of 01:34, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3dlh' size='340' side='right' caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3dlh' size='340' side='right' caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DLH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DLH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlb\|3dlb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlb\|3dlb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~274 Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [http://www.ebi.ac.uk/pdbsum/3dlh 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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [http://pdbe.org/3dlh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [http://www.ebi.ac.uk/pdbsum/3dlh PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dlh ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3dlh" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Thet2]]
	[[Category: Patel, D J]]		[[Category: Patel, D J]]
	[[Category: Sheng, G]]		[[Category: Sheng, G]]

OCA at 11:27, 20 January 2015

OCA — Tue, 20 Jan 2015 11:27:00 GMT

←Older revision		Revision as of 11:27, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3dlh\| PDB=3dlh \| SCENE= }}~~	+	==Crystal structure of the guide-strand-containing Argonaute protein silencing complex==
-	===Crystal structure of the guide-strand-containing Argonaute protein silencing complex===	+	<StructureSection load='3dlh' size='340' side='right' caption='[[3dlh]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18754009}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dlh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DLH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dlb\|3dlb]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=3dlh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dlh RCSB], [http://www.ebi.ac.uk/pdbsum/3dlh PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dlh_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

-	~~==About this~~ Structure==	+	Structure of the guide-strand-containing argonaute silencing complex.,Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ Nature. 2008 Nov 13;456(7219):209-13. Epub 2008 Aug 27. PMID:18754009<ref>PMID:18754009</ref>
-	~~[[3dlh]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3DLH OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
		+	*[[Argonaute\|Argonaute]]
	*[[RNA Interference\|RNA Interference]]		*[[RNA Interference\|RNA Interference]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018754009<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Patel, D J.]]	+	[[Category: Patel, D J]]
-	[[Category: Sheng, G.]]	+	[[Category: Sheng, G]]
-	[[Category: Wang, Y.]]	+	[[Category: Wang, Y]]
	[[Category: Argonaute]]		[[Category: Argonaute]]
	[[Category: Nucleic acid binding protein-dna complex]]		[[Category: Nucleic acid binding protein-dna complex]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

OCA at 10:59, 11 March 2013

OCA — Mon, 11 Mar 2013 10:59:53 GMT

←Older revision		Revision as of 10:59, 11 March 2013
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-	[[Image:3dlh.png\|left\|200px]]
-
	{{STRUCTURE_3dlh\| PDB=3dlh \| SCENE= }}		{{STRUCTURE_3dlh\| PDB=3dlh \| SCENE= }}
-
	===Crystal structure of the guide-strand-containing Argonaute protein silencing complex===		===Crystal structure of the guide-strand-containing Argonaute protein silencing complex===
-
	{{ABSTRACT_PUBMED_18754009}}		{{ABSTRACT_PUBMED_18754009}}

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

OCA — Mon, 07 Jan 2013 22:58:48 GMT

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

←Older revision

Revision as of 22:58, 7 January 2013

OCA at 22:58, 7 January 2013

OCA — Mon, 07 Jan 2013 22:58:45 GMT

←Older revision		Revision as of 22:58, 7 January 2013
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-	{{Seed}}
	[[Image:3dlh.png\|left\|200px]]		[[Image:3dlh.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dlh", 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_3dlh\| PDB=3dlh \| SCENE= }}		{{STRUCTURE_3dlh\| PDB=3dlh \| SCENE= }}

	===Crystal structure of the guide-strand-containing Argonaute protein silencing complex===		===Crystal structure of the guide-strand-containing Argonaute protein silencing complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18754009}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18754009 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18754009}}		{{ABSTRACT_PUBMED_18754009}}

	==About this Structure==		==About this Structure==
-	~~3DLH~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA].	+	[[3dlh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA].
		+
		+	==See Also==
		+	*[[RNA Interference\|RNA Interference]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18754009~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018754009</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Patel, D J.]]		[[Category: Patel, D J.]]
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	[[Category: Wang, Y.]]		[[Category: Wang, Y.]]
	[[Category: Argonaute]]		[[Category: Argonaute]]
-	[[Category: Nucleic acid binding protein/dna complex]]	+	[[Category: Nucleic acid binding protein-dna complex]]
-	~~[[Category: Plasmid~~]]	+
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:21:19 2009''

OCA at 12:21, 17 February 2009

OCA — Tue, 17 Feb 2009 12:21:20 GMT

←Older revision		Revision as of 12:21, 17 February 2009
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	==About this Structure==		==About this Structure==
-	3DLH is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA].	+	3DLH is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA].

	==Reference==		==Reference==
-	~~Structure of the guide-strand-containing argonaute silencing complex., Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ, Nature. 2008 Aug 27.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18754009 18754009]~~	+	<ref group="xtra">PMID:18754009</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Patel, D J.]]
		+	[[Category: Sheng, G.]]
		+	[[Category: Wang, Y.]]
	[[Category: Argonaute]]		[[Category: Argonaute]]
	[[Category: Nucleic acid binding protein/dna complex]]		[[Category: Nucleic acid binding protein/dna complex]]
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	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Dec 31 20~~:22:~~48 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:21:19 2009''

OCA at 15:00, 1 January 2009

OCA — Thu, 01 Jan 2009 15:00:52 GMT

←Older revision		Revision as of 15:00, 1 January 2009
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	==About this Structure==		==About this Structure==
-	3DLH is a ~~4 chains~~ structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA].	+	3DLH is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLH OCA].

	==Reference==		==Reference==
	Structure of the guide-strand-containing argonaute silencing complex., Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ, Nature. 2008 Aug 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18754009 18754009]		Structure of the guide-strand-containing argonaute silencing complex., Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ, Nature. 2008 Aug 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18754009 18754009]
		+	[[Category: Protein complex]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: ~~Patel~~, ~~D J.]]~~	+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-	~~[[Category~~: ~~Sheng, G.]]~~	+
-	~~[[Category: Wang, Y~~.]]	+
	[[Category: Argonaute]]		[[Category: Argonaute]]
	[[Category: Nucleic acid binding protein/dna complex]]		[[Category: Nucleic acid binding protein/dna complex]]
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	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 31 09:13:17 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 31 20:22:48 2008''