2ria - Revision history

OCA at 04:26, 2 July 2021

OCA — Fri, 02 Jul 2021 04:26:25 GMT

←Older revision		Revision as of 04:26, 2 July 2021
Line 1:		Line 1:

	==Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose==		==Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose==
-	<StructureSection load='2ria' size='340' side='right' caption='[[2ria]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2ria' size='340' side='right'caption='[[2ria]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ria]] 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=2RIA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ria]] 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=2RIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RIA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=289:D-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE'>289</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=289:D-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE'>289</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([~~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">SFTPD, PSPD, SFTP4 ([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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [~~http~~://pdbe.org/2ria PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ria PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ria 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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [https://pdbe.org/2ria PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [https://www.ebi.ac.uk/pdbsum/2ria PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ria ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.	+	[[https://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
	== 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/ri/2ria_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/2ria_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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cafarella, T]]		[[Category: Cafarella, T]]
	[[Category: Crouch, E]]		[[Category: Crouch, E]]

OCA at 07:52, 25 October 2017

OCA — Wed, 25 Oct 2017 07:52:31 GMT

←Older revision		Revision as of 07:52, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose==		==Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose==
	<StructureSection load='2ria' size='340' side='right' caption='[[2ria]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ria' size='340' side='right' caption='[[2ria]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([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">SFTPD, PSPD, SFTP4 ([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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [http://pdbe.org/2ria PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [http://www.ebi.ac.uk/pdbsum/2ria 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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [http://pdbe.org/2ria PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [http://www.ebi.ac.uk/pdbsum/2ria PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ria ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 14:19, 7 February 2016

OCA — Sun, 07 Feb 2016 14:19:08 GMT

←Older revision		Revision as of 14:19, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='2ria' size='340' side='right' caption='[[2ria]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ria' size='340' side='right' caption='[[2ria]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ria]] 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=2RIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ria]] 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=2RIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RIA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=289:D-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE'>289</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=289:D-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE'>289</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([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">SFTPD, PSPD, SFTP4 ([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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [http://www.ebi.ac.uk/pdbsum/2ria 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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [http://pdbe.org/2ria PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [http://www.ebi.ac.uk/pdbsum/2ria PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=2ria ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 2ria" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cafarella, T]]		[[Category: Cafarella, T]]
	[[Category: Crouch, E]]		[[Category: Crouch, E]]

OCA at 15:52, 24 December 2014

OCA — Wed, 24 Dec 2014 15:52:41 GMT

←Older revision		Revision as of 15:52, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ria]] 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=2RIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ria]] 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=2RIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RIA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=289:D-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE'>289</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=289:D-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE'>289</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([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">SFTPD, PSPD, SFTP4 ([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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [http://www.ebi.ac.uk/pdbsum/2ria 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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [http://www.ebi.ac.uk/pdbsum/2ria PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cafarella, T.]]	+	[[Category: Cafarella, T]]
-	[[Category: Crouch, E.]]	+	[[Category: Crouch, E]]
-	[[Category: Head, J.]]	+	[[Category: Head, J]]
-	[[Category: Kosma, P.]]	+	[[Category: Kosma, P]]
-	[[Category: McDonald, B.]]	+	[[Category: McDonald, B]]
-	[[Category: Seaton, B.]]	+	[[Category: Seaton, B]]
-	[[Category: Sheikh, S.]]	+	[[Category: Sheikh, S]]
-	[[Category: Smith, K.]]	+	[[Category: Smith, K]]
-	[[Category: Wang, H.]]	+	[[Category: Wang, H]]
	[[Category: Carbohydrate recognition]]		[[Category: Carbohydrate recognition]]
	[[Category: Domain trimeric]]		[[Category: Domain trimeric]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
	[[Category: Surfactant protein]]		[[Category: Surfactant protein]]

OCA at 04:05, 3 October 2014

OCA — Fri, 03 Oct 2014 04:05:03 GMT

←Older revision		Revision as of 04:05, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2ria\| PDB=2ria \| SCENE= }}~~	+	==Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose==
-	===Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose===	+	<StructureSection load='2ria' size='340' side='right' caption='[[2ria]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18092821}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ria]] 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=2RIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RIA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=289:D-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSE'>289</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ggu\|2ggu]], [[2ggx\|2ggx]], [[1pwq\|1pwq]], [[1pwb\|1pwb]], [[2orj\|2orj]], [[2ork\|2ork]], [[2rib\|2rib]], [[2ric\|2ric]], [[2rid\|2rid]], [[2rie\|2rie]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([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=2ria FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ria OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ria RCSB], [http://www.ebi.ac.uk/pdbsum/2ria 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/ri/2ria_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 ==
		+	Lipopolysaccharides (LPS) of Gram-negative bacteria are important mediators of bacterial virulence that can elicit potent endotoxic effects. Surfactant protein D (SP-D) shows specific interactions with LPS, both in vitro and in vivo. These interactions involve binding of the carbohydrate recognition domain (CRD) to LPS oligosaccharides (OS); however, little is known about the mechanisms of LPS recognition. Recombinant neck+CRDs (NCRDs) provide an opportunity to directly correlate binding interactions with a crystallographic analysis of the binding mechanism. In these studies, we examined the interactions of wild-type and mutant trimeric NCRDs with rough LPS (R-LPS). Although rat NCRDs bound more efficiently than human NCRDs to Escherichia coli J-5 LPS, both proteins exhibited efficient binding to solid-phase Rd2-LPS and to Rd2-LPS aggregates presented in the solution phase. Involvement of residues flanking calcium at the sugar binding site was demonstrated by reciprocal exchange of lysine and arginine at position 343 of rat and human CRDs. The lectin activity of hNCRDs was inhibited by specific heptoses, including l-glycero-alpha-d-manno-heptose (l,d-heptose), but not by 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo). Crystallographic analysis of the hNCRD demonstrated a novel binding orientation for l,d-heptose, involving the hydroxyl groups of the side chain. Similar binding was observed for a synthetic alpha1-->3-linked heptose disaccharide corresponding to heptoses I and II of the inner core region in many LPS. 7-O-Carbamoyl-l,d-heptose and d-glycero-alpha-d-manno-heptose were bound via ring hydroxyl groups. Interactions with the side chain of inner core heptoses provide a potential mechanism for the recognition of diverse types of LPS by SP-D.

-	~~==Function==~~	+	Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d.,Wang H, Head J, Kosma P, Brade H, Muller-Loennies S, Sheikh S, McDonald B, Smith K, Cafarella T, Seaton B, Crouch E Biochemistry. 2008 Jan 15;47(2):710-20. Epub 2007 Dec 20. PMID:18092821<ref>PMID:18092821</ref>
-	~~[[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in~~ the ~~extracellular reorganization or turnover~~ of ~~pulmonary~~ surfactant. ~~Binds strongly maltose residues and to a lesser extent other alpha~~-~~glucosyl moieties~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[2ria]] 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=2RIA OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:018092821</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cafarella, T.]]		[[Category: Cafarella, T.]]

OCA at 07:14, 30 June 2013

OCA — Sun, 30 Jun 2013 07:14:37 GMT

←Older revision		Revision as of 07:14, 30 June 2013
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-	[[Image:2ria.png\|left\|200px]]
-
	{{STRUCTURE_2ria\| PDB=2ria \| SCENE= }}		{{STRUCTURE_2ria\| PDB=2ria \| SCENE= }}
-
	===Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose===		===Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose===
		+	{{ABSTRACT_PUBMED_18092821}}

-	~~{{ABSTRACT_PUBMED_18092821}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.

	==About this Structure==		==About this Structure==
Line 11:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:018092821</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018092821</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cafarella, T.]]		[[Category: Cafarella, T.]]

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

OCA — Mon, 07 Jan 2013 21:55:29 GMT

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

←Older revision

Revision as of 21:55, 7 January 2013

OCA at 21:55, 7 January 2013

OCA — Mon, 07 Jan 2013 21:55:27 GMT

←Older revision		Revision as of 21:55, 7 January 2013
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-	{{Seed}}
	[[Image:2ria.png\|left\|200px]]		[[Image:2ria.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ria", 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_2ria\| PDB=2ria \| SCENE= }}		{{STRUCTURE_2ria\| PDB=2ria \| SCENE= }}

	===Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose===		===Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18092821}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18092821 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18092821}}		{{ABSTRACT_PUBMED_18092821}}

	==About this Structure==		==About this Structure==
-	~~2RIA~~ is a 3 ~~chains~~ structure ~~of 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=2RIA OCA].	+	[[2ria]] 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=2RIA OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18092821~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018092821</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cafarella, T.]]		[[Category: Cafarella, T.]]
Line 38:		Line 26:
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
	[[Category: Surfactant protein]]		[[Category: Surfactant protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:24:48 2009''

OCA at 12:24, 16 February 2009

OCA — Mon, 16 Feb 2009 12:24:49 GMT

←Older revision		Revision as of 12:24, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2RIA is a ~~[[Single protein]]~~ structure of ~~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=2RIA OCA].	+	2RIA is a 3 chains structure of 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=2RIA OCA].

	==Reference==		==Reference==
-	Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d., Wang H, Head J, Kosma P, Brade H, Muller-Loennies S, Sheikh S, McDonald B, Smith K, Cafarella T, Seaton B, Crouch E, Biochemistry. 2008 Jan 15;47(2):710-20. Epub 2007 Dec 20. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18092821 18092821]~~	+	<ref group="xtra">PMID:18092821</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Single protein]]
	[[Category: Cafarella, T.]]		[[Category: Cafarella, T.]]
	[[Category: Crouch, E.]]		[[Category: Crouch, E.]]
Line 40:		Line 39:
	[[Category: Surfactant protein]]		[[Category: Surfactant protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 17~~:02:~~12 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:24:48 2009''

OCA at 14:02, 27 July 2008

OCA — Sun, 27 Jul 2008 14:02:15 GMT

←Older revision		Revision as of 14:02, 27 July 2008
Line 1:		Line 1:
-	[[Image:2ria.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2ria.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2ria\| PDB=2ria \| SCENE= }}		{{STRUCTURE_2ria\| PDB=2ria \| SCENE= }}

-	~~'''~~Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose~~'''~~	+	===Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose===


-	~~==Overview==~~	+	<!--
-	~~Lipopolysaccharides (LPS) of Gram~~-~~negative bacteria are important mediators of bacterial virulence that can elicit potent endotoxic effects. Surfactant protein D (SP~~-~~D) shows specific interactions with LPS~~, ~~both in vitro and in vivo. These interactions involve binding of the carbohydrate recognition domain (CRD) to LPS oligosaccharides (OS); however~~, ~~little is known about~~ the ~~mechanisms of LPS recognition. Recombinant neck+CRDs (NCRDs) provide an opportunity~~ to ~~directly correlate binding interactions with a crystallographic analysis of~~ the ~~binding mechanism. In these studies, we examined the interactions of wild-type and mutant trimeric NCRDs with rough LPS~~ (~~R-LPS)~~. Although rat NCRDs bound more efficiently than human NCRDs to Escherichia coli J-5 LPS, both proteins exhibited efficient binding to solid-phase Rd2-LPS and to Rd2-LPS aggregates presented in the solution phase. Involvement of residues flanking calcium at the sugar binding site was demonstrated by reciprocal exchange of lysine and arginine at position 343 of rat and human CRDs. The lectin activity of hNCRDs was inhibited by specific heptoses, including l-glycero-alpha-d-manno-heptose (l,d-heptose), ~~but not by 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo). Crystallographic analysis of~~ the ~~hNCRD demonstrated a novel binding orientation for l,d-heptose, involving the hydroxyl groups of the side chain~~. ~~Similar binding was observed for a synthetic alpha1~~-->3-linked heptose disaccharide corresponding to heptoses I and II of the inner core region in many LPS. 7-O-Carbamoyl-l,d-heptose and d-glycero-alpha-d-manno-heptose were bound via ring hydroxyl groups. Interactions with the side chain of inner core heptoses provide a potential mechanism for the recognition of diverse types of LPS by SP-D.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18092821}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18092821 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18092821}}

	==About this Structure==		==About this Structure==
Line 35:		Line 39:
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
	[[Category: Surfactant protein]]		[[Category: Surfactant protein]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun ~~May 4 16~~:57:26 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 17:02:12 2008''