1nly - Revision history

OCA at 08:51, 10 April 2024

OCA — Wed, 10 Apr 2024 08:51:07 GMT

←Older revision		Revision as of 08:51, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1nly' size='340' side='right'caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1nly' size='340' side='right'caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1NLY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NLY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID~~-~~ADENYLATE+ESTER'>AGS</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.8Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max-height: 3em;~~'>~~[[1g6o\|1g6o]]~~</~~div~~><~~/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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [https://pdbe.org/1nly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [https://www.ebi.ac.uk/pdbsum/1nly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nly ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])~~</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [~~http~~://pdbe.org/1nly PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nly PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nly ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q7BK04_HELPX Q7BK04_HELPX]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		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=1nly 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=1nly ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The coupling of ATP binding/hydrolysis to macromolecular secretion systems is crucial to the pathogenicity of Gram-negative bacteria. We reported previously the structure of the ADP-bound form of the hexameric traffic VirB11 ATPase of the Helicobacter pylori type IV secretion system (named HP0525), and proposed that it functions as a gating molecule at the inner membrane, cycling through closed and open forms regulated by ATP binding/hydrolysis. Here, we combine crystal structures with analytical ultracentrifugation experiments to show that VirB11 ATPases indeed function as dynamic hexameric assemblies. In the absence of nucleotide, the N-terminal domains exhibit a collection of rigid-body conformations. Nucleotide binding 'locks' the hexamer into a symmetric and compact structure. We propose that VirB11s use the mechanical leverage generated by such nucleotide-dependent conformational changes to facilitate the export of substrates or the assembly of the type IV secretion apparatus. Biochemical characterization of mutant forms of HP0525 coupled with electron microscopy and in vivo assays support such hypothesis, and establish the relevance of VirB11s ATPases as drug targets against pathogenic bacteria.
-
-	VirB11 ATPases are dynamic hexameric assemblies: new insights into bacterial type IV secretion.,Savvides SN, Yeo HJ, Beck MR, Blaesing F, Lurz R, Lanka E, Buhrdorf R, Fischer W, Haas R, Waksman G EMBO J. 2003 May 1;22(9):1969-80. PMID:12727865<ref>PMID:12727865</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nly" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori]]	+	[[Category: Helicobacter pylori 26695]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beck~~, M R~~]]	+	[[Category: Beck MR]]
-	[[Category: Blaesing, F]]	+	[[Category: Blaesing F]]
-	[[Category: Buhrdorf, R]]	+	[[Category: Buhrdorf R]]
-	[[Category: Fischer, W]]	+	[[Category: Fischer W]]
-	[[Category: Haas, R]]	+	[[Category: Haas R]]
-	[[Category: Lanka, E]]	+	[[Category: Lanka E]]
-	[[Category: Lurz, R]]	+	[[Category: Lurz R]]
-	[[Category: Savvides~~, S N~~]]	+	[[Category: Savvides SN]]
-	[[Category: Waksman, G]]	+	[[Category: Waksman G]]
-	[[Category: Yeo~~, H J]]~~	+	[[Category: Yeo HJ]]
-	~~[[Category: Atpgamma]]~~	+
-	~~[[Category: Bacterial type iv secretion]]~~	+
-	~~[[Category: Helicobacter pylori]]~~	+
-	~~[[Category: Hp0525]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Virb11 atpase~~]]	+

OCA at 08:53, 2 December 2020

OCA — Wed, 02 Dec 2020 08:53:03 GMT

←Older revision		Revision as of 08:53, 2 December 2020
Line 1:		Line 1:

	==Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS==		==Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS==
-	<StructureSection load='1nly' size='340' side='right' caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1nly' size='340' side='right'caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NLY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NLY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[1g6o\|1g6o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1g6o\|1g6o]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://pdbe.org/1nly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nly ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://pdbe.org/1nly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nly ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Campylobacter pylori]]		[[Category: Campylobacter pylori]]
		+	[[Category: Large Structures]]
	[[Category: Beck, M R]]		[[Category: Beck, M R]]
	[[Category: Blaesing, F]]		[[Category: Blaesing, F]]

OCA at 07:35, 7 February 2018

OCA — Wed, 07 Feb 2018 07:35:13 GMT

←Older revision		Revision as of 07:35, 7 February 2018
Line 1:		Line 1:
		+
	==Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS==		==Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS==
	<StructureSection load='1nly' size='340' side='right' caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1nly' size='340' side='right' caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g6o\|1g6o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g6o\|1g6o]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://pdbe.org/1nly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly 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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://pdbe.org/1nly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nly ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/1nly_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/1nly_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>

OCA at 13:56, 7 February 2016

OCA — Sun, 07 Feb 2016 13:56:07 GMT

←Older revision		Revision as of 13:56, 7 February 2016
Line 17:		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=1nly ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:08, 10 September 2015

OCA — Thu, 10 Sep 2015 02:08:05 GMT

←Older revision		Revision as of 02:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1nly' size='340' side='right' caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1nly' size='340' side='right' caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Helicobacter_pylori Helicobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NLY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NLY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">[[1g6o\|1g6o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g6o\|1g6o]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~210 Helicobacter~~ pylori])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly 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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://pdbe.org/1nly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 1nly" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Helicobacter~~ pylori]]	+	[[Category: Campylobacter pylori]]
	[[Category: Beck, M R]]		[[Category: Beck, M R]]
	[[Category: Blaesing, F]]		[[Category: Blaesing, F]]
Line 44:		Line 45:
	[[Category: Atpgamma]]		[[Category: Atpgamma]]
	[[Category: Bacterial type iv secretion]]		[[Category: Bacterial type iv secretion]]
		+	[[Category: Helicobacter pylori]]
	[[Category: Hp0525]]		[[Category: Hp0525]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Virb11 atpase]]		[[Category: Virb11 atpase]]

OCA at 17:06, 5 January 2015

OCA — Mon, 05 Jan 2015 17:06:38 GMT

←Older revision		Revision as of 17:06, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NLY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NLY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g6o\|1g6o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g6o\|1g6o]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])</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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly 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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly 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 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
-	[[Category: Beck, M R.]]	+	[[Category: Beck, M R]]
-	[[Category: Blaesing, F.]]	+	[[Category: Blaesing, F]]
-	[[Category: Buhrdorf, R.]]	+	[[Category: Buhrdorf, R]]
-	[[Category: Fischer, W.]]	+	[[Category: Fischer, W]]
-	[[Category: Haas, R.]]	+	[[Category: Haas, R]]
-	[[Category: Lanka, E.]]	+	[[Category: Lanka, E]]
-	[[Category: Lurz, R.]]	+	[[Category: Lurz, R]]
-	[[Category: Savvides, S N.]]	+	[[Category: Savvides, S N]]
-	[[Category: Waksman, G.]]	+	[[Category: Waksman, G]]
-	[[Category: Yeo, H J.]]	+	[[Category: Yeo, H J]]
	[[Category: Atpgamma]]		[[Category: Atpgamma]]
	[[Category: Bacterial type iv secretion]]		[[Category: Bacterial type iv secretion]]
-	[[Category: Helicobacter pylori]]
	[[Category: Hp0525]]		[[Category: Hp0525]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Virb11 atpase]]		[[Category: Virb11 atpase]]

OCA at 10:59, 3 October 2014

OCA — Fri, 03 Oct 2014 10:59:07 GMT

←Older revision		Revision as of 10:59, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1nly\| PDB=1nly \| SCENE= }}~~	+	==Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS==
-	===Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS===	+	<StructureSection load='1nly' size='340' side='right' caption='[[1nly]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12727865}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NLY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1g6o\|1g6o]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp0525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])</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=1nly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nly OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nly RCSB], [http://www.ebi.ac.uk/pdbsum/1nly 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/nl/1nly_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 coupling of ATP binding/hydrolysis to macromolecular secretion systems is crucial to the pathogenicity of Gram-negative bacteria. We reported previously the structure of the ADP-bound form of the hexameric traffic VirB11 ATPase of the Helicobacter pylori type IV secretion system (named HP0525), and proposed that it functions as a gating molecule at the inner membrane, cycling through closed and open forms regulated by ATP binding/hydrolysis. Here, we combine crystal structures with analytical ultracentrifugation experiments to show that VirB11 ATPases indeed function as dynamic hexameric assemblies. In the absence of nucleotide, the N-terminal domains exhibit a collection of rigid-body conformations. Nucleotide binding 'locks' the hexamer into a symmetric and compact structure. We propose that VirB11s use the mechanical leverage generated by such nucleotide-dependent conformational changes to facilitate the export of substrates or the assembly of the type IV secretion apparatus. Biochemical characterization of mutant forms of HP0525 coupled with electron microscopy and in vivo assays support such hypothesis, and establish the relevance of VirB11s ATPases as drug targets against pathogenic bacteria.

-	~~==About this Structure==~~	+	VirB11 ATPases are dynamic hexameric assemblies: new insights into bacterial type IV secretion.,Savvides SN, Yeo HJ, Beck MR, Blaesing F, Lurz R, Lanka E, Buhrdorf R, Fischer W, Haas R, Waksman G EMBO J. 2003 May 1;22(9):1969-80. PMID:12727865<ref>PMID:12727865</ref>
-	~~[[1nly]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Helicobacter_pylori Helicobacter pylori]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:012727865</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
	[[Category: Beck, M R.]]		[[Category: Beck, M R.]]

OCA at 10:59, 16 April 2014

OCA — Wed, 16 Apr 2014 10:59:11 GMT

←Older revision		Revision as of 10:59, 16 April 2014
Line 1:		Line 1:
-	[[Image:1nly.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nly", 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_1nly\| PDB=1nly \| SCENE= }}		{{STRUCTURE_1nly\| PDB=1nly \| SCENE= }}
-
	===Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS===		===Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12727865}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12727865 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12727865}}		{{ABSTRACT_PUBMED_12727865}}

Line 22:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012727865</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012727865</ref><references group="xtra"/><references/>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
	[[Category: Beck, M R.]]		[[Category: Beck, M R.]]

OCA: Protected "1nly" [edit=sysop:move=sysop]

OCA — Thu, 08 Mar 2012 05:00:12 GMT

Protected "1nly" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:00, 8 March 2012

OCA at 05:00, 8 March 2012

OCA — Thu, 08 Mar 2012 05:00:10 GMT

←Older revision		Revision as of 05:00, 8 March 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1nly.png\|left\|200px]]		[[Image:1nly.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~1NLY~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Helicobacter_pylori_26695~~ Helicobacter pylori ~~26695~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA].	+	[[1nly]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12727865~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012727865</ref><references group="xtra"/>
-	[[Category: Helicobacter pylori ~~26695~~]]	+	[[Category: Helicobacter pylori]]
	[[Category: Beck, M R.]]		[[Category: Beck, M R.]]
	[[Category: Blaesing, F.]]		[[Category: Blaesing, F.]]
Line 39:		Line 38:
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
	[[Category: Hp0525]]		[[Category: Hp0525]]
		+	[[Category: Hydrolase]]
	[[Category: Virb11 atpase]]		[[Category: Virb11 atpase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:15:44 2009''