3fw5 - Revision history

OCA at 06:53, 6 September 2023

OCA — Wed, 06 Sep 2023 06:53:03 GMT

←Older revision		Revision as of 06:53, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3fw5' size='340' side='right'caption='[[3fw5]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3fw5' size='340' side='right'caption='[[3fw5]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fw5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fw5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FW5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCT:4-METHYLCATECHOL'>MCT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fw4\|3fw4]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCT:4-METHYLCATECHOL'>MCT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL, LCN2, NGAL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [https://pdbe.org/3fw5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [https://www.ebi.ac.uk/pdbsum/3fw5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fw5 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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [https://pdbe.org/3fw5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [https://www.ebi.ac.uk/pdbsum/3fw5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fw5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>	+	[https://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 32:
	==See Also==		==See Also==
	*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]		*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]
-	*[[Siderocalin\|Siderocalin]]	+	*[[Siderocalin 3D structures\|Siderocalin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Clifton~~, M C~~]]	+	[[Category: Clifton MC]]
-	[[Category: Strong~~, R K]]~~	+	[[Category: Strong RK]]
-	~~[[Category: 310-helix]]~~	+
-	~~[[Category: 8-stranded anti-parallel beta barrel]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Pyrrolidone carboxylic acid]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 19:58, 20 October 2021

OCA — Wed, 20 Oct 2021 19:58:52 GMT

←Older revision		Revision as of 19:58, 20 October 2021
Line 1:		Line 1:

	==Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol==		==Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol==
-	<StructureSection load='3fw5' size='340' side='right' caption='[[3fw5]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3fw5' size='340' side='right'caption='[[3fw5]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fw5]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fw5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FW5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCT:4-METHYLCATECHOL'>MCT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCT:4-METHYLCATECHOL'>MCT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fw4\|3fw4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fw4\|3fw4]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL, LCN2, NGAL ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL, LCN2, NGAL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [~~http~~://pdbe.org/3fw5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fw5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fw5 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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [https://pdbe.org/3fw5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [https://www.ebi.ac.uk/pdbsum/3fw5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fw5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>	+	[[https://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Clifton, M C]]		[[Category: Clifton, M C]]
	[[Category: Strong, R K]]		[[Category: Strong, R K]]

OCA at 07:58, 5 December 2018

OCA — Wed, 05 Dec 2018 07:58:32 GMT

←Older revision		Revision as of 07:58, 5 December 2018
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fw/3fw5_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fw/3fw5_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:
	==See Also==		==See Also==
	*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]		*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]
		+	*[[Siderocalin\|Siderocalin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:01, 4 August 2016

OCA — Thu, 04 Aug 2016 13:01:47 GMT

←Older revision		Revision as of 13:01, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol==		==Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol==
	<StructureSection load='3fw5' size='340' side='right' caption='[[3fw5]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3fw5' size='340' side='right' caption='[[3fw5]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fw5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fw5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FW5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCT:4-METHYLCATECHOL'>MCT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCT:4-METHYLCATECHOL'>MCT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fw4\|3fw4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fw4\|3fw4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL, LCN2, NGAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL, LCN2, NGAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [http://www.ebi.ac.uk/pdbsum/3fw5 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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [http://pdbe.org/3fw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [http://www.ebi.ac.uk/pdbsum/3fw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fw5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=3fw5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	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 3fw5" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Clifton, M C]]		[[Category: Clifton, M C]]
	[[Category: Strong, R K]]		[[Category: Strong, R K]]

OCA at 14:48, 24 December 2014

OCA — Wed, 24 Dec 2014 14:48:46 GMT

←Older revision		Revision as of 14:48, 24 December 2014
Line 8:		Line 8:
	<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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [http://www.ebi.ac.uk/pdbsum/3fw5 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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [http://www.ebi.ac.uk/pdbsum/3fw5 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:17, 3 December 2014

OCA — Wed, 03 Dec 2014 10:17:31 GMT

←Older revision		Revision as of 10:17, 3 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3fw5.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol==
		+	<StructureSection load='3fw5' size='340' side='right' caption='[[3fw5]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fw5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FW5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCT:4-METHYLCATECHOL'>MCT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fw4\|3fw4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL, LCN2, NGAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3fw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fw5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fw5 RCSB], [http://www.ebi.ac.uk/pdbsum/3fw5 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/fw/3fw5_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 lipocalins are secreted proteins that bind small organic molecules. Scn-Ngal (also known as neutrophil gelatinase associated lipocalin, siderocalin, lipocalin 2) sequesters bacterial iron chelators, called siderophores, and consequently blocks bacterial growth. However, Scn-Ngal is also prominently expressed in aseptic diseases, implying that it binds additional ligands and serves additional functions. Using chemical screens, crystallography and fluorescence methods, we report that Scn-Ngal binds iron together with a small metabolic product called catechol. The formation of the complex blocked the reactivity of iron and permitted its transport once introduced into circulation in vivo. Scn-Ngal then recycled its iron in endosomes by a pH-sensitive mechanism. As catechols derive from bacterial and mammalian metabolism of dietary compounds, the Scn-Ngal-catechol-Fe(III) complex represents an unforeseen microbial-host interaction, which mimics Scn-Ngal-siderophore interactions but instead traffics iron in aseptic tissues. These results identify an endogenous siderophore, which may link the disparate roles of Scn-Ngal in different diseases.

-	~~{{STRUCTURE_3fw5\| PDB=3fw5 \| SCENE= }}~~	+	Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex.,Bao G, Clifton M, Hoette TM, Mori K, Deng SX, Qiu A, Viltard M, Williams D, Paragas N, Leete T, Kulkarni R, Li X, Lee B, Kalandadze A, Ratner AJ, Pizarro JC, Schmidt-Ott KM, Landry DW, Raymond KN, Strong RK, Barasch J Nat Chem Biol. 2010 Aug;6(8):602-9. Epub 2010 Jun 27. PMID:20581821<ref>PMID:20581821</ref>

-	~~===Crystal structure of Siderocalin (NGAL~~, ~~Lipocalin 2) complexed with Ferric 4-methyl-catechol===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_20581821}}~~	+	==See Also==
-		+	*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3fw5~~]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:020581821<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Clifton, M C.]]	+	[[Category: Clifton, M C]]
-	[[Category: Strong, R K.]]	+	[[Category: Strong, R K]]
	[[Category: 310-helix]]		[[Category: 310-helix]]
	[[Category: 8-stranded anti-parallel beta barrel]]		[[Category: 8-stranded anti-parallel beta barrel]]

OCA: Protected "3fw5" [edit=sysop:move=sysop]

OCA — Wed, 20 Feb 2013 14:36:24 GMT

Protected "3fw5" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:36, 20 February 2013

OCA at 14:36, 20 February 2013

OCA — Wed, 20 Feb 2013 14:36:20 GMT

←Older revision		Revision as of 14:36, 20 February 2013
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-	{{Seed}}
	[[Image:3fw5.png\|left\|200px]]		[[Image:3fw5.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fw5", 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_3fw5\| PDB=3fw5 \| SCENE= }}		{{STRUCTURE_3fw5\| PDB=3fw5 \| SCENE= }}

	===Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol===		===Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20581821}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20581821 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20581821}}		{{ABSTRACT_PUBMED_20581821}}

	==About this Structure==		==About this Structure==
-	~~3FW5~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA].	+	[[3fw5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20581821~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020581821</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Clifton, M C.]]		[[Category: Clifton, M C.]]
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	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Transport protein]]		[[Category: Transport protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Aug 12 00:05:11 2010''

OCA at 19:57, 11 August 2010

OCA — Wed, 11 Aug 2010 19:57:54 GMT

←Older revision		Revision as of 19:57, 11 August 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3fw5.~~jpg~~\|left\|200px]]	+	[[Image:3fw5.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol===		===Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20581821}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20581821 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20581821}}

	==About this Structure==		==About this Structure==
	3FW5 is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA].		3FW5 is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20581821</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Clifton, M C.]]		[[Category: Clifton, M C.]]
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	[[Category: Transport protein]]		[[Category: Transport protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed May 5~~ 12:05:03 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Aug 12 00:05:11 2010''

OCA at 09:05, 5 May 2010

OCA — Wed, 05 May 2010 09:05:04 GMT

←Older revision		Revision as of 09:05, 5 May 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3fw5.jpg\|left\|200px]]

-	The ~~entry 3fw5~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3fw5", 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_3fw5\| PDB=3fw5 \| SCENE= }}

-	~~Authors: Clifton~~, ~~M.C., Strong, R.K.~~	+	===Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol===

-	Description: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 18 08~~:53:~~45 2009~~''	+	==About this Structure==
		+	3FW5 is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FW5 OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Clifton, M C.]]
		+	[[Category: Strong, R K.]]
		+	[[Category: 310-helix]]
		+	[[Category: 8-stranded anti-parallel beta barrel]]
		+	[[Category: Glycoprotein]]
		+	[[Category: Pyrrolidone carboxylic acid]]
		+	[[Category: Secreted]]
		+	[[Category: Transport protein]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 12:05:03 2010''