2xr5 - Revision history

OCA at 08:02, 23 August 2023

2023-08-23T08:02:51Z

←Older revision		Revision as of 08:02, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='2xr5' size='340' side='right'caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='2xr5' size='340' side='right'caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xr5]] is a 1 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=2XR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XR5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xr5]] is a 1 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=2XR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XR5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.42Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b6b\|2b6b]], [[2xr6\|2xr6]], [[1sl4\|1sl4]], [[1k9i\|1k9i]], [[1sl5\|1sl5]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [https://pdbe.org/2xr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [https://www.ebi.ac.uk/pdbsum/2xr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xr5 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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [https://pdbe.org/2xr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [https://www.ebi.ac.uk/pdbsum/2xr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xr5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN]] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref> On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>	+	[https://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref> On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernardi, A]]	+	[[Category: Bernardi A]]
-	[[Category: Fieschi, F]]	+	[[Category: Fieschi F]]
-	[[Category: Reina, J]]	+	[[Category: Reina J]]
-	[[Category: Sattin, S]]	+	[[Category: Sattin S]]
-	[[Category: Suitkeviciute, I]]	+	[[Category: Suitkeviciute I]]
-	[[Category: Thepaut, M]]	+	[[Category: Thepaut M]]
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 14:53, 17 November 2021

2021-11-17T14:53:14Z

←Older revision		Revision as of 14:53, 17 November 2021
Line 1:		Line 1:

	==Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.==		==Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.==
-	<StructureSection load='2xr5' size='340' side='right' caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>	+	<StructureSection load='2xr5' size='340' side='right'caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xr5]] 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=2XR5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2XR5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xr5]] is a 1 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=2XR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XR5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b6b\|2b6b]], [[2xr6\|2xr6]], [[1sl4\|1sl4]], [[1k9i\|1k9i]], [[1sl5\|1sl5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b6b\|2b6b]], [[2xr6\|2xr6]], [[1sl4\|1sl4]], [[1k9i\|1k9i]], [[1sl5\|1sl5]]</div></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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [~~http~~://pdbe.org/2xr5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2xr5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2xr5 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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [https://pdbe.org/2xr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [https://www.ebi.ac.uk/pdbsum/2xr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xr5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN]] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref> On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>	+	[[https://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN]] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref> On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bernardi, A]]		[[Category: Bernardi, A]]
	[[Category: Fieschi, F]]		[[Category: Fieschi, F]]

OCA at 07:58, 6 March 2019

2019-03-06T07:58:17Z

←Older revision		Revision as of 07:58, 6 March 2019
Line 1:		Line 1:

	==Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.==		==Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.==
-	<StructureSection load='2xr5' size='340' side='right' caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>	+	<StructureSection load='2xr5' size='340' side='right' caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2xr5]] 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=2XR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XR5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2xr5]] 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=2XR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XR5 FirstGlance]. <br>

OCA at 00:03, 5 August 2016

2016-08-05T00:03:28Z

←Older revision		Revision as of 00:03, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.==		==Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.==
	<StructureSection load='2xr5' size='340' side='right' caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='2xr5' size='340' side='right' caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b6b\|2b6b]], [[2xr6\|2xr6]], [[1sl4\|1sl4]], [[1k9i\|1k9i]], [[1sl5\|1sl5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b6b\|2b6b]], [[2xr6\|2xr6]], [[1sl4\|1sl4]], [[1k9i\|1k9i]], [[1sl5\|1sl5]]</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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2xr5 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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [http://pdbe.org/2xr5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2xr5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xr5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 2xr5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:13, 25 December 2014

2014-12-25T14:13:33Z

←Older revision		Revision as of 14:13, 25 December 2014
Line 7:		Line 7:
	<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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2xr5 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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2xr5 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN]] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref> On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:25, 21 December 2014

2014-12-21T16:25:48Z

←Older revision		Revision as of 16:25, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2xr5\| PDB=2xr5 \| SCENE= }}~~	+	==Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.==
-	===Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.===	+	<StructureSection load='2xr5' size='340' side='right' caption='[[2xr5]], [[Resolution\|resolution]] 1.42Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23360500}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2xr5]] 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=2XR5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XR5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b6b\|2b6b]], [[2xr6\|2xr6]], [[1sl4\|1sl4]], [[1k9i\|1k9i]], [[1sl5\|1sl5]]</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=2xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xr5 RCSB], [http://www.ebi.ac.uk/pdbsum/2xr5 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In genital mucosa, different fates are described for HIV according to the subtype of dendritic cells (DCs) involved in its recognition. This notably depends on the C-type lectin receptor, langerin or DC-SIGN, involved in gp120 interaction. Langerin blocks HIV transmission by its internalization in specific organelles of Langerhans cells. On the contrary, DC-SIGN enhances HIV trans-infection of T lymphocytes. Thus, approaches aiming to inhibit DC-SIGN, without blocking langerin, represent attractive anti-HIV strategies. We previously demonstrated that dendrons bearing multiple copies of glycomimetic compounds were able to block DC-SIGN-dependent HIV infection in cervical explant models. Optimization of such ligand requires detailed characterization of its binding mode. In the present work, we determined the first high-resolution structure of a glycomimetic/DC-SIGN complex by X-ray crystallography. This glycomimetic, pseudo-1,2-mannobioside, shares shape and conformational properties with Manalpha1-2Man, its natural counterpart. However, it uses the binding epitope previously described for Lewis X, a ligand specific for DC-SIGN among the C-type lectin family. Thus, selectivity gain for DC-SIGN versus langerin is observed with pseudo-1,2-mannobioside as shown by surface plasmon resonance analysis. In parallel, ligand binding was also analyzed by TR-NOESY and STD NMR experiments, combined with the CORCEMA-ST protocol. These studies demonstrate that the complex, defined by X-ray crystallography, represents the unique binding mode of this ligand as opposed to the several binding orientations described for the natural ligand. This exclusive binding mode and its selective interaction properties position this glycomimetic as a good lead compound for rational improvement based on a structurally driven approach.

-	~~==Function==~~	+	Structure of a glycomimetic ligand in the carbohydrate recognition domain of C-type lectin DC-SIGN. Structural requirements for selectivity and ligand design.,Thepaut M, Guzzi C, Sutkeviciute I, Sattin S, Ribeiro-Viana R, Varga N, Chabrol E, Rojo J, Bernardi A, Angulo J, Nieto PM, Fieschi F J Am Chem Soc. 2013 Feb 20;135(7):2518-29. doi: 10.1021/ja3053305. Epub 2013 Feb , 8. PMID:23360500<ref>PMID:23360500</ref>
-	~~[[http://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN]] Pathogen-recognition receptor expressed on the surface~~ of ~~immature dendritic cells (DCs) and involved~~ in ~~initiation of primary immune response. Thought to mediate~~ the ~~endocytosis~~ of ~~pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen~~-~~derived antigens are presented to resting T~~-~~cells via MHC class II proteins to initiate the adaptive immune response~~. ~~Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens~~, ~~including HIV-1 gp120~~, ~~HIV-2 gp120~~, ~~SIV gp120~~, ~~ebolavirus glycoproteins~~, ~~cytomegalovirus gB~~, ~~HCV E2~~, ~~dengue virus gE~~, ~~Leishmania pifanoi LPG~~, ~~Lewis-x antigen in Helicobacter pylori LPS~~, ~~mannose in Klebsiella pneumonae LPS~~, di-~~mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA~~.~~<ref>PMID~~:~~10721995<~~/ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref> On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. ~~May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2~~. ~~Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>~~PMID:~~10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref>~~ <ref>PMID:~~12574325~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2xr5]] 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=2XR5 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023360500</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Bernardi, A.]]	+	[[Category: Bernardi, A]]
-	[[Category: Fieschi, F.]]	+	[[Category: Fieschi, F]]
-	[[Category: Reina, J.]]	+	[[Category: Reina, J]]
-	[[Category: Sattin, S.]]	+	[[Category: Sattin, S]]
-	[[Category: Suitkeviciute, I.]]	+	[[Category: Suitkeviciute, I]]
-	[[Category: Thepaut, M.]]	+	[[Category: Thepaut, M]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 08:49, 25 December 2013

2013-12-25T08:49:26Z

←Older revision		Revision as of 08:49, 25 December 2013
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-	[[Image:2xr5.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_2xr5", 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_2xr5\| PDB=2xr5 \| SCENE= }}		{{STRUCTURE_2xr5\| PDB=2xr5 \| SCENE= }}
		+	===Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.===
		+	{{ABSTRACT_PUBMED_23360500}}

-	===~~CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN~~ DC-~~SIGN WITH PSEUDO DIMANNOSIDE MIMIC~~.~~===~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN]] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref> On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>

		+	==About this Structure==
		+	[[2xr5]] 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=2XR5 OCA].

-	==~~About this Structure~~==	+	==Reference==
-	~~[[2xr5]] 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=2XR5 OCA].~~	+	<ref group="xtra">PMID:023360500</ref><references group="xtra"/><references/>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Bernardi, A.]]		[[Category: Bernardi, A.]]
	[[Category: Fieschi, F.]]		[[Category: Fieschi, F.]]

OCA: Protected "2xr5" [edit=sysop:move=sysop]

2011-10-30T10:09:37Z

Protected "2xr5" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:09, 30 October 2011

OCA at 10:09, 30 October 2011

2011-10-30T10:09:31Z

←Older revision		Revision as of 10:09, 30 October 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:2xr5.png\|left\|200px]]

-	The ~~entry 2xr5~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2xr5", 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_2xr5\| PDB=2xr5 \| SCENE= }}

-	~~Authors: THEPAUT, M., SUITKEVICIUTE, I., SATTIN, S., REINA, J., BERNARDI, A., FIESCHI, F~~.	+	===CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN DC-SIGN WITH PSEUDO DIMANNOSIDE MIMIC.===

-	Description: Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Oct 6 05~~:41:~~47 2010''~~	+	==About this Structure==
		+	[[2xr5]] 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=2XR5 OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Bernardi, A.]]
		+	[[Category: Fieschi, F.]]
		+	[[Category: Reina, J.]]
		+	[[Category: Sattin, S.]]
		+	[[Category: Suitkeviciute, I.]]
		+	[[Category: Thepaut, M.]]
		+	[[Category: Sugar binding protein]]

OCA at 02:32, 6 October 2010

2010-10-06T02:32:16Z

←Older revision		Revision as of 02:32, 6 October 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 2xr5 is ON HOLD	+	The entry 2xr5 is ON HOLD until Paper Publication

	Authors: THEPAUT, M., SUITKEVICIUTE, I., SATTIN, S., REINA, J., BERNARDI, A., FIESCHI, F.		Authors: THEPAUT, M., SUITKEVICIUTE, I., SATTIN, S., REINA, J., BERNARDI, A., FIESCHI, F.
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	Description: Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.		Description: Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 22 14~~:26:38 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 6 05:41:47 2010''