2gxu - Revision history

OCA at 09:30, 14 February 2024

OCA — Wed, 14 Feb 2024 09:30:22 GMT

←Older revision		Revision as of 09:30, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='2gxu' size='340' side='right'caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='2gxu' size='340' side='right'caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gxu]] is a 1 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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gxu]] is a 1 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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GXU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.67Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[2gxq\|2gxq]], [[2gxs\|2gxs]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">HERA ([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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [https://pdbe.org/2gxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [https://www.ebi.ac.uk/pdbsum/2gxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gxu 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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [https://pdbe.org/2gxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [https://www.ebi.ac.uk/pdbsum/2gxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gxu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O07897_THETH O07897_THETH]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=2gxu 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=2gxu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DEAD box RNA helicases use the energy of ATP hydrolysis to unwind double-stranded RNA regions or to disrupt RNA/protein complexes. A minimal RNA helicase comprises nine conserved motifs distributed over two RecA-like domains. The N-terminal domain contains all motifs involved in nucleotide binding, namely the Q-motif, the DEAD box, and the P-loop, as well as the SAT motif, which has been implicated in the coordination of ATP hydrolysis and RNA unwinding. We present here the crystal structure of the N-terminal domain of the Thermus thermophilus RNA helicase Hera in complex with adenosine monophosphate (AMP). Upon binding of AMP the P-loop adopts a partially collapsed or half-open conformation that is still connected to the DEAD box motif, and the DEAD box in turn is linked to the SAT motif via hydrogen bonds. This network of interactions communicates changes in the P-loop conformation to distant parts of the helicase. The affinity of AMP is comparable to that of ADP and ATP, substantiating that the binding energy from additional phosphate moieties is directly converted into conformational changes of the entire helicase. Importantly, the N-terminal Hera domain forms a dimer in the crystal similar to that seen in another thermophilic prokaryote. It is possible that this mode of dimerization represents the prototypic architecture in RNA helicases of thermophilic origin.
-
-	Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain.,Rudolph MG, Heissmann R, Wittmann JG, Klostermeier D J Mol Biol. 2006 Aug 25;361(4):731-43. Epub 2006 Jul 12. PMID:16890241<ref>PMID:16890241</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2gxu" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet2~~]]	+	[[Category: Thermus thermophilus HB27]]
-	[[Category: Klostermeier, D]]	+	[[Category: Klostermeier D]]
-	[[Category: Rudolph~~, M G]]~~	+	[[Category: Rudolph MG]]
-	~~[[Category: Amp complex]]~~	+
-	~~[[Category: Atomic resolution]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ribosome biogenesis]]~~	+
-	~~[[Category: Rna helicase]]~~	+
-	~~[[Category: Thermophilic~~]]	+

OCA at 07:26, 17 March 2021

OCA — Wed, 17 Mar 2021 07:26:31 GMT

←Older revision		Revision as of 07:26, 17 March 2021
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	==HERA N-terminal domain in complex with orthophosphate, crystal form 1==		==HERA N-terminal domain in complex with orthophosphate, crystal form 1==
-	<StructureSection load='2gxu' size='340' side='right' caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>	+	<StructureSection load='2gxu' size='340' side='right'caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gxu]] is a 1 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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2GXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gxu]] is a 1 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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GXU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2gxq\|2gxq]], [[2gxs\|2gxs]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HERA ([~~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">HERA ([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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [~~http~~://pdbe.org/2gxu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2gxu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2gxu 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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [https://pdbe.org/2gxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [https://www.ebi.ac.uk/pdbsum/2gxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gxu ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/2gxu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/2gxu_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 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet2]]		[[Category: Thet2]]
	[[Category: Klostermeier, D]]		[[Category: Klostermeier, D]]

OCA at 08:03, 18 October 2017

OCA — Wed, 18 Oct 2017 08:03:05 GMT

←Older revision		Revision as of 08:03, 18 October 2017
Line 1:		Line 1:
		+
	==HERA N-terminal domain in complex with orthophosphate, crystal form 1==		==HERA N-terminal domain in complex with orthophosphate, crystal form 1==
	<StructureSection load='2gxu' size='340' side='right' caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='2gxu' size='340' side='right' caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HERA ([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">HERA ([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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [http://pdbe.org/2gxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [http://www.ebi.ac.uk/pdbsum/2gxu 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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [http://pdbe.org/2gxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [http://www.ebi.ac.uk/pdbsum/2gxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gxu ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=2gxu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:19, 11 September 2015

OCA — Fri, 11 Sep 2015 13:19:41 GMT

←Older revision		Revision as of 13:19, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2gxu' size='340' side='right' caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='2gxu' size='340' side='right' caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gxu]] is a 1 chain structure with sequence from [http://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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GXU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gxu]] is a 1 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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GXU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HERA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 ~~Thermus thermophilus HB27~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HERA ([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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [http://www.ebi.ac.uk/pdbsum/2gxu 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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [http://pdbe.org/2gxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [http://www.ebi.ac.uk/pdbsum/2gxu PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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 2gxu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus hb27~~]]	+	[[Category: Thet2]]
	[[Category: Klostermeier, D]]		[[Category: Klostermeier, D]]
	[[Category: Rudolph, M G]]		[[Category: Rudolph, M G]]

OCA at 09:25, 16 January 2015

OCA — Fri, 16 Jan 2015 09:25:28 GMT

←Older revision		Revision as of 09:25, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gxu]] is a 1 chain structure with sequence from [http://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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GXU FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gxu]] is a 1 chain structure with sequence from [http://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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GXU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HERA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 Thermus thermophilus HB27])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HERA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 Thermus thermophilus HB27])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [http://www.ebi.ac.uk/pdbsum/2gxu 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=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [http://www.ebi.ac.uk/pdbsum/2gxu PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus hb27]]		[[Category: Thermus thermophilus hb27]]
-	[[Category: Klostermeier, D.]]	+	[[Category: Klostermeier, D]]
-	[[Category: Rudolph, M G.]]	+	[[Category: Rudolph, M G]]
	[[Category: Amp complex]]		[[Category: Amp complex]]
	[[Category: Atomic resolution]]		[[Category: Atomic resolution]]

OCA at 10:53, 30 September 2014

OCA — Tue, 30 Sep 2014 10:53:01 GMT

←Older revision		Revision as of 10:53, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2gxu.~~png~~\|~~left~~\|200px]]	+	==HERA N-terminal domain in complex with orthophosphate, crystal form 1==
		+	<StructureSection load='2gxu' size='340' side='right' caption='[[2gxu]], [[Resolution\|resolution]] 1.67Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2gxu]] is a 1 chain structure with sequence from [http://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=2GXU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GXU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gxq\|2gxq]], [[2gxs\|2gxs]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HERA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 Thermus thermophilus HB27])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gxu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gxu RCSB], [http://www.ebi.ac.uk/pdbsum/2gxu 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/gx/2gxu_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 ==
		+	DEAD box RNA helicases use the energy of ATP hydrolysis to unwind double-stranded RNA regions or to disrupt RNA/protein complexes. A minimal RNA helicase comprises nine conserved motifs distributed over two RecA-like domains. The N-terminal domain contains all motifs involved in nucleotide binding, namely the Q-motif, the DEAD box, and the P-loop, as well as the SAT motif, which has been implicated in the coordination of ATP hydrolysis and RNA unwinding. We present here the crystal structure of the N-terminal domain of the Thermus thermophilus RNA helicase Hera in complex with adenosine monophosphate (AMP). Upon binding of AMP the P-loop adopts a partially collapsed or half-open conformation that is still connected to the DEAD box motif, and the DEAD box in turn is linked to the SAT motif via hydrogen bonds. This network of interactions communicates changes in the P-loop conformation to distant parts of the helicase. The affinity of AMP is comparable to that of ADP and ATP, substantiating that the binding energy from additional phosphate moieties is directly converted into conformational changes of the entire helicase. Importantly, the N-terminal Hera domain forms a dimer in the crystal similar to that seen in another thermophilic prokaryote. It is possible that this mode of dimerization represents the prototypic architecture in RNA helicases of thermophilic origin.

-	~~{{STRUCTURE_2gxu\| PDB=2gxu \| SCENE= }}~~	+	Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain.,Rudolph MG, Heissmann R, Wittmann JG, Klostermeier D J Mol Biol. 2006 Aug 25;361(4):731-43. Epub 2006 Jul 12. PMID:16890241<ref>PMID:16890241</ref>

-	~~===HERA N-terminal domain in complex with orthophosphate~~, ~~crystal form 1===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16890241}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2gxu]] is~~ a ~~1 chain structure with sequence from [http://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=2GXU OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016890241<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus hb27]]		[[Category: Thermus thermophilus hb27]]
	[[Category: Klostermeier, D.]]		[[Category: Klostermeier, D.]]

OCA: Protected "2gxu" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 12:39:45 GMT

Protected "2gxu" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:39, 7 January 2013

OCA at 12:39, 7 January 2013

OCA — Mon, 07 Jan 2013 12:39:41 GMT

←Older revision		Revision as of 12:39, 7 January 2013
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-	{{Seed}}
	[[Image:2gxu.png\|left\|200px]]		[[Image:2gxu.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2gxu\| PDB=2gxu \| SCENE= }}		{{STRUCTURE_2gxu\| PDB=2gxu \| SCENE= }}

	===HERA N-terminal domain in complex with orthophosphate, crystal form 1===		===HERA N-terminal domain in complex with orthophosphate, crystal form 1===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16890241}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16890241 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_16890241}}		{{ABSTRACT_PUBMED_16890241}}

	==About this Structure==		==About this Structure==
-	~~2GXU~~ is a 1 chain structure of 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=2GXU OCA].	+	[[2gxu]] is a 1 chain structure with sequence from [http://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=2GXU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16890241~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016890241</ref><references group="xtra"/>
-	[[Category: Thermus thermophilus]]	+	[[Category: Thermus thermophilus hb27]]
	[[Category: Klostermeier, D.]]		[[Category: Klostermeier, D.]]
	[[Category: Rudolph, M G.]]		[[Category: Rudolph, M G.]]
	[[Category: Amp complex]]		[[Category: Amp complex]]
	[[Category: Atomic resolution]]		[[Category: Atomic resolution]]
		+	[[Category: Hydrolase]]
	[[Category: Ribosome biogenesis]]		[[Category: Ribosome biogenesis]]
	[[Category: Rna helicase]]		[[Category: Rna helicase]]
	[[Category: Thermophilic]]		[[Category: Thermophilic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:33:57 2009''

OCA at 20:33, 17 February 2009

OCA — Tue, 17 Feb 2009 20:33:59 GMT

←Older revision		Revision as of 20:33, 17 February 2009
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	==About this Structure==		==About this Structure==
-	2GXU is a ~~[[Single protein]]~~ structure of 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=2GXU OCA].	+	2GXU is a 1 chain structure of 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=2GXU OCA].

	==Reference==		==Reference==
-	Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain., Rudolph MG, Heissmann R, Wittmann JG, Klostermeier D, J Mol Biol. 2006 Aug 25;361(4):731-43. Epub 2006 Jul 12. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16890241 16890241]~~	+	<ref group="xtra">PMID:16890241</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Klostermeier, D.]]		[[Category: Klostermeier, D.]]
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	[[Category: Thermophilic]]		[[Category: Thermophilic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 06~~:43:~~42 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:33:57 2009''

OCA at 03:43, 29 July 2008

OCA — Tue, 29 Jul 2008 03:43:45 GMT

←Older revision		Revision as of 03:43, 29 July 2008
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-	[[Image:2gxu.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2gxu.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2gxu\| PDB=2gxu \| SCENE= }}		{{STRUCTURE_2gxu\| PDB=2gxu \| SCENE= }}

-	~~'''~~HERA N-terminal domain in complex with orthophosphate, crystal form 1~~'''~~	+	===HERA N-terminal domain in complex with orthophosphate, crystal form 1===


-	~~==Overview==~~	+	<!--
-	~~DEAD box RNA helicases use the energy of ATP hydrolysis to unwind double~~-~~stranded RNA regions or to disrupt RNA/protein complexes. A minimal RNA helicase comprises nine conserved motifs distributed over two RecA~~-~~like domains.~~ The ~~N-terminal domain contains all motifs involved in nucleotide binding~~, ~~namely the Q-motif~~, the ~~DEAD box, and~~ the ~~P-loop,~~ as ~~well as the SAT motif, which has been implicated in the coordination of ATP hydrolysis and RNA unwinding~~. ~~We present here the crystal structure of the N-terminal domain of the Thermus thermophilus RNA helicase Hera in complex with adenosine monophosphate (AMP~~)~~. Upon binding of AMP the P-loop adopts a partially collapsed or half-open conformation that is still connected to the DEAD box motif~~, ~~and the DEAD box in turn~~ is ~~linked to~~ the ~~SAT motif via hydrogen bonds~~. ~~This network of interactions communicates changes in the P~~-loop conformation to distant parts of the helicase. The affinity of AMP is comparable to that of ADP and ATP, substantiating that the binding energy from additional phosphate moieties is directly converted into conformational changes of the entire helicase. Importantly, the N-terminal Hera domain forms a dimer in the crystal similar to that seen in another thermophilic prokaryote. It is possible that this mode of dimerization represents the prototypic architecture in RNA helicases of thermophilic origin.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16890241}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16890241 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16890241}}

	==About this Structure==		==About this Structure==
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	[[Category: Rna helicase]]		[[Category: Rna helicase]]
	[[Category: Thermophilic]]		[[Category: Thermophilic]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 05~~:39:00 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:43:42 2008''