1ji4 - Revision history

OCA at 08:41, 16 August 2023

2023-08-16T08:41:16Z

← Older revision		Revision as of 08:41, 16 August 2023
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	<StructureSection load='1ji4' size='340' side='right'caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='1ji4' size='340' side='right'caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43504 Atcc 43504~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 2.52Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dps\|1dps]], [[1qgh\|1qgh]]</div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])~~</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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [https://pdbe.org/1ji4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [~~http~~://pdbe.org/1ji4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/DPS_HELPY DPS_HELPY]] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). Required for the survival in the presence of oxidative stress. Dps is also a virulence factor that activates neutrophils, mast cells and monocytes. It binds to neutrophil-glycosphingolipids and to sulfated carbohydrates on mucin. It might have a role in the accumulation of neutrophils and monocytes at the site of infection. Induces superoxide anion generation, adhesion and chemotaxis of neutrophils, through a pertussis toxin-sensitive pathway involving MAP kinases.<ref>PMID:11069248</ref> <ref>PMID:7768601</ref> <ref>PMID:10790422</ref> <ref>PMID:11857341</ref> <ref>PMID:12672049</ref> <ref>PMID:12748264</ref>		[https://www.uniprot.org/uniprot/DPS_HELPY DPS_HELPY] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). Required for the survival in the presence of oxidative stress. Dps is also a virulence factor that activates neutrophils, mast cells and monocytes. It binds to neutrophil-glycosphingolipids and to sulfated carbohydrates on mucin. It might have a role in the accumulation of neutrophils and monocytes at the site of infection. Induces superoxide anion generation, adhesion and chemotaxis of neutrophils, through a pertussis toxin-sensitive pathway involving MAP kinases.<ref>PMID:11069248</ref> <ref>PMID:7768601</ref> <ref>PMID:10790422</ref> <ref>PMID:11857341</ref> <ref>PMID:12672049</ref> <ref>PMID:12748264</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 43504~~]]		[[Category: Helicobacter pylori]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Battistutta, R]]		[[Category: Battistutta R]]
	[[Category: ~~Dundon, W~~ G]]		[[Category: Del Giudice G]]
	[[Category: ~~Giudice, G Del~~]]		[[Category: Dundon WG]]
	[[Category: Montecucco, C]]		[[Category: Montecucco C]]
	[[Category: Papinutto, E]]		[[Category: Papinutto E]]
	[[Category: Rappuoli, R]]		[[Category: Rappuoli R]]
	[[Category: Seveso, M]]		[[Category: Seveso M]]
	[[Category: Zanotti, G]]		[[Category: Zanotti G]]
	~~[[Category: Dodecamer]]~~
	~~[[Category: Four-helix bundle]]~~
	~~[[Category: Metal transport~~]]

OCA at 07:31, 25 November 2020

2020-11-25T07:31:50Z

← Older revision		Revision as of 07:31, 25 November 2020
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	==NAP protein from helicobacter pylori==		==NAP protein from helicobacter pylori==
	<StructureSection load='1ji4' size='340' side='right' caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='1ji4' size='340' side='right'caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dps\|1dps]], [[1qgh\|1qgh]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://pdbe.org/1ji4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://pdbe.org/1ji4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1ji4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ji4" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Ferritin 3D structures\|Ferritin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 43504]]		[[Category: Atcc 43504]]
			[[Category: Large Structures]]
	[[Category: Battistutta, R]]		[[Category: Battistutta, R]]
	[[Category: Dundon, W G]]		[[Category: Dundon, W G]]

OCA at 08:49, 17 January 2018

2018-01-17T08:49:51Z

← Older revision		Revision as of 08:49, 17 January 2018
Line 1:		Line 1:

	==NAP protein from helicobacter pylori==		==NAP protein from helicobacter pylori==
	<StructureSection load='1ji4' size='340' side='right' caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='1ji4' size='340' side='right' caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://pdbe.org/1ji4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://pdbe.org/1ji4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/1ji4_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/1ji4_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>
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	</div>		</div>
	<div class="pdbe-citations 1ji4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ji4" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Ferritin\|Ferritin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:34, 9 February 2016

2016-02-09T18:34:30Z

← Older revision		Revision as of 18:34, 9 February 2016
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	<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=1ji4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:56, 11 September 2015

2015-09-11T00:56:14Z

← Older revision		Revision as of 00:56, 11 September 2015
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	<StructureSection load='1ji4' size='340' side='right' caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='1ji4' size='340' side='right' caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ji4]] is a 12 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=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([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">NAPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://pdbe.org/1ji4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1ji4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Helicobacter pylori~~]]		[[Category: Atcc 43504]]
	[[Category: Battistutta, R]]		[[Category: Battistutta, R]]
	[[Category: Dundon, W G]]		[[Category: Dundon, W G]]

OCA at 08:42, 25 December 2014

2014-12-25T08:42:46Z

← Older revision		Revision as of 08:42, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ji4]] is a 12 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=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ji4]] is a 12 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=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([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">NAPA ([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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DPS_HELPY DPS_HELPY]] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). Required for the survival in the presence of oxidative stress. Dps is also a virulence factor that activates neutrophils, mast cells and monocytes. It binds to neutrophil-glycosphingolipids and to sulfated carbohydrates on mucin. It might have a role in the accumulation of neutrophils and monocytes at the site of infection. Induces superoxide anion generation, adhesion and chemotaxis of neutrophils, through a pertussis toxin-sensitive pathway involving MAP kinases.<ref>PMID:11069248</ref> <ref>PMID:7768601</ref> <ref>PMID:10790422</ref> <ref>PMID:11857341</ref> <ref>PMID:12672049</ref> <ref>PMID:12748264</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
	[[Category: Battistutta, R.]]		[[Category: Battistutta, R]]
	[[Category: Dundon, W G.]]		[[Category: Dundon, W G]]
	[[Category: Giudice, G Del.]]		[[Category: Giudice, G Del]]
	[[Category: Montecucco, C.]]		[[Category: Montecucco, C]]
	[[Category: Papinutto, E.]]		[[Category: Papinutto, E]]
	[[Category: Rappuoli, R.]]		[[Category: Rappuoli, R]]
	[[Category: Seveso, M.]]		[[Category: Seveso, M]]
	[[Category: Zanotti, G.]]		[[Category: Zanotti, G]]
	[[Category: Dodecamer]]		[[Category: Dodecamer]]
	[[Category: Four-helix bundle]]		[[Category: Four-helix bundle]]
	[[Category: Metal transport]]		[[Category: Metal transport]]

OCA at 10:57, 28 September 2014

2014-09-28T10:57:46Z

← Older revision		Revision as of 10:57, 28 September 2014
Line 1:		Line 1:
	[[Image:~~1ji4~~.~~png~~\|~~left~~\|~~200px~~]]		==NAP protein from helicobacter pylori==
			<StructureSection load='1ji4' size='340' side='right' caption='[[1ji4]], [[Resolution\|resolution]] 2.52Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1ji4]] is a 12 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=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dps\|1dps]], [[1qgh\|1qgh]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAPA ([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=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 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/ji/1ji4_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 ==
			Helicobacter pylori is a major human pathogen associated with severe gastroduodenal diseases, including ulcers and cancers. An H.pylori protein that is highly immunogenic in humans and mice has been identified recently. This protein has been termed HP-NAP, due to its ability of activating neutrophils. In order to achieve a molecular understanding of its unique immunogenic and pro-inflammatory properties, we have determined its three-dimensional structure. Its quaternary structure is similar to that of the dodecameric bacterial ferritins (Dps-like family), but it has a different surface potential charge distribution. This is due to the presence of a large number of positively charged residues, which could well account for its unique ability in activating human leukocytes.

	~~{{STRUCTURE_1ji4\| PDB=1ji4 \| SCENE= }}~~		Structure of the neutrophil-activating protein from Helicobacter pylori.,Zanotti G, Papinutto E, Dundon W, Battistutta R, Seveso M, Giudice G, Rappuoli R, Montecucco C J Mol Biol. 2002 Oct 11;323(1):125-30. PMID:12368104<ref>PMID:12368104</ref>

	~~===NAP protein from helicobacter pylori===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_12368104}}~~

	~~==About this Structure==~~
	~~[[1ji4]] is~~ a ~~12 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=1JI4 OCA].~~

	==See Also==		==See Also==
	*[[Ferritin\|Ferritin]]		*[[Ferritin\|Ferritin]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:012368104<~~/~~ref~~><~~ref group="xtra">PMID:016345079</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
	[[Category: Battistutta, R.]]		[[Category: Battistutta, R.]]

OCA at 14:45, 20 October 2012

2012-10-20T14:45:05Z

← Older revision		Revision as of 14:45, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[1ji4]] is a 12 chain structure ~~of [[Ferritin]]~~ 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=1JI4 OCA].		[[1ji4]] is a 12 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=1JI4 OCA].

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
	<ref group="xtra">PMID:012368104~~</ref><ref group="xtra">PMID:012527302~~</ref><ref group="xtra">PMID:016345079</ref><references group="xtra"/>		<ref group="xtra">PMID:012368104</ref><ref group="xtra">PMID:016345079</ref><references group="xtra"/>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
	[[Category: Battistutta, R.]]		[[Category: Battistutta, R.]]

OCA at 16:07, 26 July 2012

2012-07-26T16:07:13Z

← Older revision		Revision as of 16:07, 26 July 2012
Line 1:		Line 1:
	[[Image:1ji4.png\|left\|200px]]		[[Image:1ji4.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1ji4", 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_1ji4\| PDB=1ji4 \| SCENE= }}		{{STRUCTURE_1ji4\| PDB=1ji4 \| SCENE= }}

	===NAP protein from helicobacter pylori===		===NAP protein from helicobacter pylori===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_12368104}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 12368104 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_12368104}}		{{ABSTRACT_PUBMED_12368104}}

Line 22:		Line 11:

	==See Also==		==See Also==
	*[[Ferritin]]		*[[Ferritin\|Ferritin]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~12368104~~</ref><references group="xtra"/>		<ref group="xtra">PMID:012368104</ref><ref group="xtra">PMID:012527302</ref><ref group="xtra">PMID:016345079</ref><references group="xtra"/>
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
	[[Category: Battistutta, R.]]		[[Category: Battistutta, R.]]

OCA: Protected "1ji4" [edit=sysop:move=sysop]

2010-12-26T22:36:02Z

Protected "1ji4" [edit=sysop:move=sysop]

← Older revision	Revision as of 22:36, 26 December 2010
(No difference)