2z63 - Revision history

OCA at 13:23, 1 November 2023

OCA — Wed, 01 Nov 2023 13:23:11 GMT

←Older revision		Revision as of 13:23, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2z63' size='340' side='right'caption='[[2z63]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2z63' size='340' side='right'caption='[[2z63]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bdellostoma_burgeri Bdellostoma~~ burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Eptatretus_burgeri Eptatretus burgeri] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FUL:BETA~~-~~L-FUCOSE'>FUL</scene>~~, ~~<scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">TLR4, VLRB.61 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7764 Bdellostoma burgeri])~~</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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [https://pdbe.org/2z63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [https://www.ebi.ac.uk/pdbsum/2z63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z63 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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [https://pdbe.org/2z63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [https://www.ebi.ac.uk/pdbsum/2z63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z63 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[https://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.	+	[https://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[https://omim.org/entry/611488 611488]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. Also involved in LPS-independent inflammatory responses triggered by Ni(2+). These responses require non-conserved histidines and are, therefore, species-specific.<ref>PMID:20711192</ref>	+	[https://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN] Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. Also involved in LPS-independent inflammatory responses triggered by Ni(2+). These responses require non-conserved histidines and are, therefore, species-specific.<ref>PMID:20711192</ref> [https://www.uniprot.org/uniprot/Q4G1L2_EPTBU Q4G1L2_EPTBU]
	== 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: ~~Bdellostoma~~ burgeri]]	+	[[Category: Eptatretus burgeri]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, H M~~]]	+	[[Category: Kim HM]]
-	[[Category: Lee, J O]]	+	[[Category: Lee J-O]]
-	[[Category: Park~~, B S]]~~	+	[[Category: Park BS]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Lp]]~~	+
-	~~[[Category: Md-2]]~~	+
-	~~[[Category: Tlr4]]~~	+
-	~~[[Category: Toll-like receptor~~]]	+

OCA at 10:46, 8 December 2021

OCA — Wed, 08 Dec 2021 10:46:38 GMT

←Older revision		Revision as of 10:46, 8 December 2021
Line 1:		Line 1:

	==Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61==		==Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61==
-	<StructureSection load='2z63' size='340' side='right' caption='[[2z63]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2z63' size='340' side='right'caption='[[2z63]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z63]] is a 1 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=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellostoma_burgeri Bdellostoma burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TLR4, VLRB.61 ([~~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">TLR4, VLRB.61 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7764 Bdellostoma burgeri])</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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [~~http~~://pdbe.org/2z63 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z63 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z63 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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [https://pdbe.org/2z63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [https://www.ebi.ac.uk/pdbsum/2z63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z63 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[~~http~~://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.	+	[[https://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[https://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. Also involved in LPS-independent inflammatory responses triggered by Ni(2+). These responses require non-conserved histidines and are, therefore, species-specific.<ref>PMID:20711192</ref>	+	[[https://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. Also involved in LPS-independent inflammatory responses triggered by Ni(2+). These responses require non-conserved histidines and are, therefore, species-specific.<ref>PMID:20711192</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z6/2z63_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z6/2z63_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 34:		Line 34:

	==See Also==		==See Also==
-	*[[Toll-like ~~Receptors~~\|Toll-like ~~Receptors~~]]	+	*[[Toll-like Receptor 3D structures\|Toll-like Receptor 3D structures]]
-	*[[Variable lymphocyte receptor\|Variable lymphocyte receptor]]	+	*[[Variable lymphocyte receptor 3D structures\|Variable lymphocyte receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Bdellostoma burgeri]]
		+	[[Category: Large Structures]]
	[[Category: Kim, H M]]		[[Category: Kim, H M]]
	[[Category: Lee, J O]]		[[Category: Lee, J O]]

OCA at 16:00, 11 August 2016

OCA — Thu, 11 Aug 2016 16:00:09 GMT

←Older revision		Revision as of 16:00, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61==		==Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61==
	<StructureSection load='2z63' size='340' side='right' caption='[[2z63]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2z63' size='340' side='right' caption='[[2z63]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z63]] is a 1 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=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z63]] is a 1 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=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TLR4, VLRB.61 ([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">TLR4, VLRB.61 ([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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [http://www.ebi.ac.uk/pdbsum/2z63 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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [http://pdbe.org/2z63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [http://www.ebi.ac.uk/pdbsum/2z63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z63 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 21:
	<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=2z63 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	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 2z63" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 40:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Kim, H M]]		[[Category: Kim, H M]]
	[[Category: Lee, J O]]		[[Category: Lee, J O]]

OCA at 10:04, 20 January 2015

OCA — Tue, 20 Jan 2015 10:04:36 GMT

←Older revision		Revision as of 10:04, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z63]] is a 1 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=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z63]] is a 1 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=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TLR4, VLRB.61 ([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">TLR4, VLRB.61 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [http://www.ebi.ac.uk/pdbsum/2z63 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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [http://www.ebi.ac.uk/pdbsum/2z63 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[http://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.		[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[http://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Kim, H M.]]	+	[[Category: Kim, H M]]
-	[[Category: Lee, J O.]]	+	[[Category: Lee, J O]]
-	[[Category: Park, B S.]]	+	[[Category: Park, B S]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Lp]]		[[Category: Lp]]

OCA at 04:49, 2 October 2014

OCA — Thu, 02 Oct 2014 04:49:43 GMT

←Older revision		Revision as of 04:49, 2 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2z63\| PDB=2z63 \| SCENE= }}~~	+	==Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61==
-	===Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61===	+	<StructureSection load='2z63' size='340' side='right' caption='[[2z63]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17803912}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[2z63]] is a 1 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=2Z63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z63 FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z62\|2z62]], [[2z64\|2z64]], [[2z65\|2z65]], [[2z66\|2z66]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TLR4, VLRB.61 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2z63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z63 RCSB], [http://www.ebi.ac.uk/pdbsum/2z63 PDBsum]</span></td></tr>
		+	<table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[http://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.		[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[http://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. Also involved in LPS-independent inflammatory responses triggered by Ni(2+). These responses require non-conserved histidines and are, therefore, species-specific.<ref>PMID:20711192</ref>
		+	== 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/z6/2z63_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 ==
		+	TLR4 and MD-2 form a heterodimer that recognizes LPS (lipopolysaccharide) from Gram-negative bacteria. Eritoran is an analog of LPS that antagonizes its activity by binding to the TLR4-MD-2 complex. We determined the structure of the full-length ectodomain of the mouse TLR4 and MD-2 complex. We also produced a series of hybrids of human TLR4 and hagfish VLR and determined their structures with and without bound MD-2 and Eritoran. TLR4 is an atypical member of the LRR family and is composed of N-terminal, central, and C-terminal domains. The beta sheet of the central domain shows unusually small radii and large twist angles. MD-2 binds to the concave surface of the N-terminal and central domains. The interaction with Eritoran is mediated by a hydrophobic internal pocket in MD-2. Based on structural analysis and mutagenesis experiments on MD-2 and TLR4, we propose a model of TLR4-MD-2 dimerization induced by LPS.

-	~~==Function==~~	+	Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran.,Kim HM, Park BS, Kim JI, Kim SE, Lee J, Oh SC, Enkhbayar P, Matsushima N, Lee H, Yoo OJ, Lee JO Cell. 2007 Sep 7;130(5):906-17. PMID:17803912<ref>PMID:17803912</ref>
-	~~[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Cooperates with LY96 and CD14 to mediate~~ the ~~innate immune response to bacterial lipopolysaccharide (LPS)~~. ~~Acts via MYD88~~, ~~TIRAP and TRAF6~~, ~~leading to NF-kappa-B activation~~, ~~cytokine secretion and the inflammatory response~~. ~~Also involved in LPS-independent inflammatory responses triggered by Ni~~(2+)~~. These responses require non~~-~~conserved histidines and are, therefore, species-specific~~.<ref>PMID:~~20711192~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2z63]] is~~ a ~~1 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=2Z63 OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Toll-like Receptors\|Toll-like Receptors]]		*[[Toll-like Receptors\|Toll-like Receptors]]
	*[[Variable lymphocyte receptor\|Variable lymphocyte receptor]]		*[[Variable lymphocyte receptor\|Variable lymphocyte receptor]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:017803912</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Kim, H M.]]		[[Category: Kim, H M.]]

OCA at 01:06, 25 March 2013

OCA — Mon, 25 Mar 2013 01:06:27 GMT

←Older revision		Revision as of 01:06, 25 March 2013
Line 1:		Line 1:
-	[[Image:2z63.png\|left\|200px]]
-
	{{STRUCTURE_2z63\| PDB=2z63 \| SCENE= }}		{{STRUCTURE_2z63\| PDB=2z63 \| SCENE= }}
-
	===Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61===		===Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61===
		+	{{ABSTRACT_PUBMED_17803912}}

-	~~{{ABSTRACT_PUBMED_17803912}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Genetic variation in TLR4 is associated with age-related macular degeneration type 10 (ARMD10) [MIM:[http://omim.org/entry/611488 611488]]. ARMD is a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane.
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/TLR4_HUMAN TLR4_HUMAN]] Cooperates with LY96 and CD14 to mediate the innate immune response to bacterial lipopolysaccharide (LPS). Acts via MYD88, TIRAP and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. Also involved in LPS-independent inflammatory responses triggered by Ni(2+). These responses require non-conserved histidines and are, therefore, species-specific.<ref>PMID:20711192</ref>

	==About this Structure==		==About this Structure==
Line 15:		Line 17:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:017803912</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017803912</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Kim, H M.]]		[[Category: Kim, H M.]]

OCA at 20:53, 20 October 2012

OCA — Sat, 20 Oct 2012 20:53:22 GMT

←Older revision		Revision as of 20:53, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2z63]] is a 1 chain structure ~~of [[Toll-like Receptors]] and [[Variable lymphocyte receptor]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens~~,_eptatretus_burgeri~~ Homo sapiens~~, eptatretus burgeri~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA].	+	[[2z63]] is a 1 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=2Z63 OCA].

	==See Also==		==See Also==
Line 16:		Line 16:
	==Reference==		==Reference==
	<ref group="xtra">PMID:017803912</ref><references group="xtra"/>		<ref group="xtra">PMID:017803912</ref><references group="xtra"/>
-	[[Category: Homo sapiens~~, eptatretus burgeri~~]]	+	[[Category: Homo sapiens]]
	[[Category: Kim, H M.]]		[[Category: Kim, H M.]]
	[[Category: Lee, J O.]]		[[Category: Lee, J O.]]

OCA: Protected "2z63" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 11:56:31 GMT

Protected "2z63" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:56, 27 July 2012

OCA at 11:56, 27 July 2012

OCA — Fri, 27 Jul 2012 11:56:30 GMT

←Older revision		Revision as of 11:56, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z63.png\|left\|200px]]		[[Image:2z63.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z63", 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_2z63\| PDB=2z63 \| SCENE= }}		{{STRUCTURE_2z63\| PDB=2z63 \| SCENE= }}

	===Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61===		===Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17803912}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17803912 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17803912}}		{{ABSTRACT_PUBMED_17803912}}

	==About this Structure==		==About this Structure==
-	~~2Z63~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens,_eptatretus_burgeri Homo sapiens, eptatretus burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA].	+	[[2z63]] is a 1 chain structure of [[Toll-like Receptors]] and [[Variable lymphocyte receptor]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens,_eptatretus_burgeri Homo sapiens, eptatretus burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA].
		+
		+	==See Also==
		+	*[[Toll-like Receptors\|Toll-like Receptors]]
		+	*[[Variable lymphocyte receptor\|Variable lymphocyte receptor]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17803912~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017803912</ref><references group="xtra"/>
	[[Category: Homo sapiens, eptatretus burgeri]]		[[Category: Homo sapiens, eptatretus burgeri]]
	[[Category: Kim, H M.]]		[[Category: Kim, H M.]]
Line 33:		Line 25:
	[[Category: Tlr4]]		[[Category: Tlr4]]
	[[Category: Toll-like receptor]]		[[Category: Toll-like receptor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 21 09:49:42 2010''

OCA at 05:43, 21 July 2010

OCA — Wed, 21 Jul 2010 05:43:17 GMT

←Older revision		Revision as of 05:43, 21 July 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z63 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens,_eptatretus_burgeri Homo sapiens, eptatretus burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA].	+	2Z63 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens,_eptatretus_burgeri Homo sapiens, eptatretus burgeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z63 OCA].

	==Reference==		==Reference==
Line 34:		Line 34:
	[[Category: Toll-like receptor]]		[[Category: Toll-like receptor]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 18 05~~:32:~~41 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 21 09:49:42 2010''