1xkp - Revision history

OCA at 14:12, 9 May 2024

OCA — Thu, 09 May 2024 14:12:04 GMT

←Older revision		Revision as of 14:12, 9 May 2024
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	<StructureSection load='1xkp' size='340' side='right'caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1xkp' size='340' side='right'caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus~~ pestis~~" (lehmann and neumann 1896) migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XKP FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=DMG:N,N~~-~~DIMETHYLGLYCINE'>DMG</scene>~~, ~~<scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</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]] 1.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yopN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~632~~ "~~Bacillus pestis~~" ~~(Lehmann and Neumann 1896) Migula 1900])~~, ~~sycN ([https:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [https://pdbe.org/1xkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [https://www.ebi.ac.uk/pdbsum/1xkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xkp 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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [https://pdbe.org/1xkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [https://www.ebi.ac.uk/pdbsum/1xkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~YSCB_YERPE YSCB_YERPE~~]~~] Functions as~~ a ~~specific chaperone for YopN~~. ~~It could facilitate~~ the ~~secretion~~ and ~~the subsequent translocation of YopN.<ref>PMID:9733695</ref> <ref>PMID:10094626</ref> <ref>PMID:12535078</ref> [[https://www.uniprot.org/uniprot/SYCN_YERPE SYCN_YERPE]] Functions as~~ a ~~specific chaperone for YopN. It could facilitate~~ the ~~secretion and the subsequent translocation of YopN~~.~~<ref>PMID:10094626</ref> <ref>PMID:12535078</ref>~~	+	[https://www.uniprot.org/uniprot/YOPN_YERPE YOPN_YERPE] Plays a major role in regulation of the low-calcium response. Seems to sense the calcium concentration and to transmit a signal to shut off yop transcription when the calcium concentration is high (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cherry, S]]	+	[[Category: Yersinia pestis]]
-	[[Category: Jackson~~, M W~~]]	+	[[Category: Cherry S]]
-	[[Category: Penrose~~, K J~~]]	+	[[Category: Jackson MW]]
-	[[Category: Plano~~, G V~~]]	+	[[Category: Penrose KJ]]
-	[[Category: Schubot~~, F D~~]]	+	[[Category: Plano GV]]
-	[[Category: Tropea~~, J E~~]]	+	[[Category: Schubot FD]]
-	[[Category: Waugh~~, D S]]~~	+	[[Category: Tropea JE]]
-	~~[[Category: Chaperone]]~~	+	[[Category: Waugh DS]]
-	~~[[Category: Membrane protein-chaperon complex]]~~	+
-	~~[[Category: Sycn]]~~	+
-	~~[[Category: Type iii secretion]]~~	+
-	~~[[Category: Yopn]]~~	+
-	~~[[Category: Yscb~~]]	+

OCA at 16:41, 20 October 2021

OCA — Wed, 20 Oct 2021 16:41:56 GMT

←Older revision		Revision as of 16:41, 20 October 2021
Line 3:		Line 3:
	<StructureSection load='1xkp' size='340' side='right'caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1xkp' size='340' side='right'caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XKP FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), sycN ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), sycN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [~~http~~://pdbe.org/1xkp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xkp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xkp 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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [https://pdbe.org/1xkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [https://www.ebi.ac.uk/pdbsum/1xkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/YSCB_YERPE YSCB_YERPE]] Functions as a specific chaperone for YopN. It could facilitate the secretion and the subsequent translocation of YopN.<ref>PMID:9733695</ref> <ref>PMID:10094626</ref> <ref>PMID:12535078</ref> [[~~http~~://www.uniprot.org/uniprot/SYCN_YERPE SYCN_YERPE]] Functions as a specific chaperone for YopN. It could facilitate the secretion and the subsequent translocation of YopN.<ref>PMID:10094626</ref> <ref>PMID:12535078</ref>	+	[[https://www.uniprot.org/uniprot/YSCB_YERPE YSCB_YERPE]] Functions as a specific chaperone for YopN. It could facilitate the secretion and the subsequent translocation of YopN.<ref>PMID:9733695</ref> <ref>PMID:10094626</ref> <ref>PMID:12535078</ref> [[https://www.uniprot.org/uniprot/SYCN_YERPE SYCN_YERPE]] Functions as a specific chaperone for YopN. It could facilitate the secretion and the subsequent translocation of YopN.<ref>PMID:10094626</ref> <ref>PMID:12535078</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:05, 6 January 2021

OCA — Wed, 06 Jan 2021 10:05:14 GMT

←Older revision		Revision as of 10:05, 6 January 2021
Line 1:		Line 1:

	==Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB==		==Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB==
-	<StructureSection load='1xkp' size='340' side='right' caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1xkp' size='340' side='right'caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XKP FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://pdbe.org/1xkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xkp 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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://pdbe.org/1xkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cherry, S]]		[[Category: Cherry, S]]
	[[Category: Jackson, M W]]		[[Category: Jackson, M W]]

OCA at 07:27, 18 April 2018

OCA — Wed, 18 Apr 2018 07:27:06 GMT

←Older revision		Revision as of 07:27, 18 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB==		==Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB==
	<StructureSection load='1xkp' size='340' side='right' caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1xkp' size='340' side='right' caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://pdbe.org/1xkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp 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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://pdbe.org/1xkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xkp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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/xk/1xkp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xk/1xkp_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>
	</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=1xkp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:07, 12 September 2015

OCA — Sat, 12 Sep 2015 00:07:02 GMT

←Older revision		Revision as of 00:07, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1xkp' size='340' side='right' caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1xkp' size='340' side='right' caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Yersinia_pestis Yersinia~~ pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XKP FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 ~~Yersinia~~ pestis]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 ~~Yersinia~~ pestis]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 ~~Yersinia~~ pestis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp 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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://pdbe.org/1xkp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1xkp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Yersinia pestis]]
	[[Category: Cherry, S]]		[[Category: Cherry, S]]
	[[Category: Jackson, M W]]		[[Category: Jackson, M W]]

OCA at 21:12, 25 December 2014

OCA — Thu, 25 Dec 2014 21:12:18 GMT

←Older revision		Revision as of 21:12, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XKP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis])</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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp 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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YSCB_YERPE YSCB_YERPE]] Functions as a specific chaperone for YopN. It could facilitate the secretion and the subsequent translocation of YopN.<ref>PMID:9733695</ref> <ref>PMID:10094626</ref> <ref>PMID:12535078</ref> [[http://www.uniprot.org/uniprot/SYCN_YERPE SYCN_YERPE]] Functions as a specific chaperone for YopN. It could facilitate the secretion and the subsequent translocation of YopN.<ref>PMID:10094626</ref> <ref>PMID:12535078</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]
-	[[Category: Cherry, S.]]	+	[[Category: Cherry, S]]
-	[[Category: Jackson, M W.]]	+	[[Category: Jackson, M W]]
-	[[Category: Penrose, K J.]]	+	[[Category: Penrose, K J]]
-	[[Category: Plano, G V.]]	+	[[Category: Plano, G V]]
-	[[Category: Schubot, F D.]]	+	[[Category: Schubot, F D]]
-	[[Category: Tropea, J E.]]	+	[[Category: Tropea, J E]]
-	[[Category: Waugh, D S.]]	+	[[Category: Waugh, D S]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
	[[Category: Membrane protein-chaperon complex]]		[[Category: Membrane protein-chaperon complex]]

OCA at 20:37, 29 September 2014

OCA — Mon, 29 Sep 2014 20:37:23 GMT

←Older revision		Revision as of 20:37, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xkp.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB==
		+	<StructureSection load='1xkp' size='340' side='right' caption='[[1xkp]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XKP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMG:N,N-DIMETHYLGLYCINE'>DMG</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis]), sycN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis]), yscB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis])</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=1xkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xkp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xkp RCSB], [http://www.ebi.ac.uk/pdbsum/1xkp 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/xk/1xkp_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 ==
		+	Yersinia pestis, the causative agent of plague, utilizes a type III secretion system (T3SS) to inject effector proteins directly into the cytosol of mammalian cells where they interfere with signal transduction pathways that regulate actin cytoskeleton dynamics and inflammation, thereby enabling the bacterium to avoid engulfment and destruction by macrophages. Type III secretion normally does not occur in the absence of close contact with eukaryotic cells. Negative regulation is mediated in part by a multiprotein complex that has been proposed to act as a physical impediment to type III secretion by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. This complex is composed of YopN, its heterodimeric secretion chaperone SycN-YscB, and TyeA. Here, we report two crystal structures of YopN in complex with its heterodimeric secretion chaperone SycN-YscB and the co-regulatory protein TyeA, respectively. By merging these two overlapping structures, it was possible to construct a credible theoretical model of the YopN-SycN-YscB-TyeA complex. The modeled assembly features the secretion signaling elements of YopN at one end of an elongated structure and the secretion regulating TyeA binding site at the other. A patch of highly conserved residues on the surface of the C-terminal alpha-helix of TyeA may mediate its interaction with structural components of the secretion apparatus. Conserved arginine residues that reside inside a prominent cavity at the dimer interface of SycN-YscB were mutated in order to investigate whether they play a role in targeting the YopN-chaperone complex to the type III secretion apparatus. One of the mutants exhibited a phenotype that is consistent with this hypothesis.

-	~~{{STRUCTURE_1xkp\| PDB=1xkp \| SCENE= }}~~	+	Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis.,Schubot FD, Jackson MW, Penrose KJ, Cherry S, Tropea JE, Plano GV, Waugh DS J Mol Biol. 2005 Mar 4;346(4):1147-61. Epub 2005 Jan 20. PMID:15701523<ref>PMID:15701523</ref>

-	~~===Crystal structure~~ of the ~~virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15701523}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xkp]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Yersinia_pestis Yersinia pestis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015701523<~~/~~ref~~><~~ref group="xtra">PMID:015502305</ref><references group="xtra"~~/>	+
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]
	[[Category: Cherry, S.]]		[[Category: Cherry, S.]]

OCA at 12:22, 23 January 2013

OCA — Wed, 23 Jan 2013 12:22:07 GMT

←Older revision		Revision as of 12:22, 23 January 2013
Line 1:		Line 1:
	[[Image:1xkp.png\|left\|200px]]		[[Image:1xkp.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xkp", 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_1xkp\| PDB=1xkp \| SCENE= }}		{{STRUCTURE_1xkp\| PDB=1xkp \| SCENE= }}

	===Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB===		===Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15701523}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15701523 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15701523}}		{{ABSTRACT_PUBMED_15701523}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15701523~~</ref><ref group="xtra">PMID:~~15502305~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015701523</ref><ref group="xtra">PMID:015502305</ref><references group="xtra"/>
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]
	[[Category: Cherry, S.]]		[[Category: Cherry, S.]]
Line 32:		Line 21:
	[[Category: Waugh, D S.]]		[[Category: Waugh, D S.]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
-	[[Category: Membrane protein/chaperon complex]]	+	[[Category: Membrane protein-chaperon complex]]
	[[Category: Sycn]]		[[Category: Sycn]]
	[[Category: Type iii secretion]]		[[Category: Type iii secretion]]
	[[Category: Yopn]]		[[Category: Yopn]]
	[[Category: Yscb]]		[[Category: Yscb]]

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

OCA — Mon, 14 Mar 2011 19:00:19 GMT

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

←Older revision

Revision as of 19:00, 14 March 2011

OCA at 19:00, 14 March 2011

OCA — Mon, 14 Mar 2011 19:00:17 GMT

←Older revision		Revision as of 19:00, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xkp.png\|left\|200px]]		[[Image:1xkp.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~1XKP~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA].	+	[[1xkp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XKP OCA].

	==Reference==		==Reference==
Line 33:		Line 32:
	[[Category: Waugh, D S.]]		[[Category: Waugh, D S.]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
		+	[[Category: Membrane protein/chaperon complex]]
	[[Category: Sycn]]		[[Category: Sycn]]
	[[Category: Type iii secretion]]		[[Category: Type iii secretion]]
	[[Category: Yopn]]		[[Category: Yopn]]
	[[Category: Yscb]]		[[Category: Yscb]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:45:18 2009''