2duq - Revision history

OCA at 08:30, 25 October 2023

OCA — Wed, 25 Oct 2023 08:30:24 GMT

←Older revision		Revision as of 08:30, 25 October 2023
Line 1:		Line 1:

	==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form==		==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form==
-	<StructureSection load='2duq' size='340' side='right'caption='[[2duq]]' scene=''>	+	<StructureSection load='2duq' size='340' side='right'caption='[[2duq]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>
-	</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [https://pdbe.org/2duq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [https://www.ebi.ac.uk/pdbsum/2duq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2duq ProSAT]</span></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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [https://pdbe.org/2duq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [https://www.ebi.ac.uk/pdbsum/2duq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2duq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LMAN2_CANLF LMAN2_CANLF] Plays a role as an intracellular lectin in the early secretory pathway. Interacts with N-acetyl-D-galactosamine and high-mannose type glycans and may also bind to O-linked glycans. Involved in the transport and sorting of glycoproteins carrying high mannose-type glycans.<ref>PMID:11872745</ref> <ref>PMID:17652092</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 20:
	</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=2duq 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=2duq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	VIP36 functions as a transport lectin for trafficking certain high mannose type glycoproteins in the secretory pathway. Here we report the crystal structure of VIP36 exoplasmic/luminal domain comprising a carbohydrate recognition domain and a stalk domain. The structures of VIP36 in complex with Ca(2+) and mannosyl ligands are also described. The carbohydrate recognition domain is composed of a 17-stranded antiparallel beta-sandwich and binds one Ca(2+) adjoining the carbohydrate-binding site. The structure reveals that a coordinated Ca(2+) ion orients the side chains of Asp(131), Asn(166), and His(190) for carbohydrate binding. This result explains the Ca(2+)-dependent carbohydrate binding of this protein. The Man-alpha-1,2-Man-alpha-1,2-Man, which corresponds to the D1 arm of high mannose type glycan, is recognized by eight residues through extensive hydrogen bonds. The complex structures reveal the structural basis for high mannose type glycoprotein recognition by VIP36 in a Ca(2+)-dependent and D1 arm-specific manner.
		+
		+	Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36.,Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S J Biol Chem. 2007 Sep 21;282(38):28246-55. Epub 2007 Jul 25. PMID:17652092<ref>PMID:17652092</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 2duq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Canis lupus familiaris]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cowieson NP]]		[[Category: Cowieson NP]]

OCA at 10:35, 17 February 2021

OCA — Wed, 17 Feb 2021 10:35:35 GMT

←Older revision		Revision as of 10:35, 17 February 2021
Line 1:		Line 1:

	==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form==		==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form==
-	<StructureSection load='2duq' size='340' side='right' caption='[[2duq]]~~, [[Resolution\|resolution]] 1.80Å~~' scene=''>	+	<StructureSection load='2duq' size='340' side='right'caption='[[2duq]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canlf Canlf].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>	+	</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [https://pdbe.org/2duq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [https://www.ebi.ac.uk/pdbsum/2duq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2duq ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 CANLF])</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [~~http~~://pdbe.org/2duq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2duq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2duq ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/LMAN2_CANFA LMAN2_CANFA]] Plays a role as an intracellular lectin in the early secretory pathway. Interacts with N-acetyl-D-galactosamine and high-mannose type glycans and may also bind to O-linked glycans. Involved in the transport and sorting of glycoproteins carrying high mannose-type glycans.<ref>PMID:11872745</ref> <ref>PMID:17652092</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 16:
	</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=2duq 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=2duq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	VIP36 functions as a transport lectin for trafficking certain high mannose type glycoproteins in the secretory pathway. Here we report the crystal structure of VIP36 exoplasmic/luminal domain comprising a carbohydrate recognition domain and a stalk domain. The structures of VIP36 in complex with Ca(2+) and mannosyl ligands are also described. The carbohydrate recognition domain is composed of a 17-stranded antiparallel beta-sandwich and binds one Ca(2+) adjoining the carbohydrate-binding site. The structure reveals that a coordinated Ca(2+) ion orients the side chains of Asp(131), Asn(166), and His(190) for carbohydrate binding. This result explains the Ca(2+)-dependent carbohydrate binding of this protein. The Man-alpha-1,2-Man-alpha-1,2-Man, which corresponds to the D1 arm of high mannose type glycan, is recognized by eight residues through extensive hydrogen bonds. The complex structures reveal the structural basis for high mannose type glycoprotein recognition by VIP36 in a Ca(2+)-dependent and D1 arm-specific manner.
-
-	Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36.,Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S J Biol Chem. 2007 Sep 21;282(38):28246-55. Epub 2007 Jul 25. PMID:17652092<ref>PMID:17652092</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2duq" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Canlf~~]]	+	[[Category: Large Structures]]
-	[[Category: Cowieson~~, N P~~]]	+	[[Category: Cowieson NP]]
-	[[Category: Kato, R]]	+	[[Category: Kato R]]
-	[[Category: Satoh, T]]	+	[[Category: Satoh T]]
-	[[Category: Wakatsuki, S]]	+	[[Category: Wakatsuki S]]
-	~~[[Category: Beta sandwich]]~~	+
-	~~[[Category: Carbohydrate binding protein]]~~	+
-	~~[[Category: Cargo receptor]]~~	+
-	~~[[Category: Protein transport~~]]	+

OCA at 06:41, 6 June 2018

OCA — Wed, 06 Jun 2018 06:41:06 GMT

←Older revision		Revision as of 06:41, 6 June 2018
Line 1:		Line 1:
		+
	==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form==		==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form==
	<StructureSection load='2duq' size='340' side='right' caption='[[2duq]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2duq' size='340' side='right' caption='[[2duq]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Canfa Canfa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canlf Canlf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 ~~CANFA~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 CANLF])</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [http://pdbe.org/2duq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [http://www.ebi.ac.uk/pdbsum/2duq 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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [http://pdbe.org/2duq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [http://www.ebi.ac.uk/pdbsum/2duq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2duq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2duq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2duq_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>
	</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=2duq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Canfa~~]]	+	[[Category: Canlf]]
	[[Category: Cowieson, N P]]		[[Category: Cowieson, N P]]
	[[Category: Kato, R]]		[[Category: Kato, R]]

OCA at 17:28, 11 September 2015

OCA — Fri, 11 Sep 2015 17:28:15 GMT

←Older revision		Revision as of 17:28, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2duq' size='340' side='right' caption='[[2duq]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2duq' size='340' side='right' caption='[[2duq]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Canis_lupus_familiaris Canis lupus familiaris~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canfa Canfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 ~~Canis lupus familiaris~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 CANFA])</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [http://www.ebi.ac.uk/pdbsum/2duq 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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [http://pdbe.org/2duq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [http://www.ebi.ac.uk/pdbsum/2duq PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 2duq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Canis lupus familiaris~~]]	+	[[Category: Canfa]]
	[[Category: Cowieson, N P]]		[[Category: Cowieson, N P]]
	[[Category: Kato, R]]		[[Category: Kato, R]]

OCA at 19:36, 25 December 2014

OCA — Thu, 25 Dec 2014 19:36:58 GMT

←Older revision		Revision as of 19:36, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 Canis lupus familiaris])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 Canis lupus familiaris])</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [http://www.ebi.ac.uk/pdbsum/2duq 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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [http://www.ebi.ac.uk/pdbsum/2duq PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LMAN2_CANFA LMAN2_CANFA]] Plays a role as an intracellular lectin in the early secretory pathway. Interacts with N-acetyl-D-galactosamine and high-mannose type glycans and may also bind to O-linked glycans. Involved in the transport and sorting of glycoproteins carrying high mannose-type glycans.<ref>PMID:11872745</ref> <ref>PMID:17652092</ref>
	== 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: Canis lupus familiaris]]		[[Category: Canis lupus familiaris]]
-	[[Category: Cowieson, N P.]]	+	[[Category: Cowieson, N P]]
-	[[Category: Kato, R.]]	+	[[Category: Kato, R]]
-	[[Category: Satoh, T.]]	+	[[Category: Satoh, T]]
-	[[Category: Wakatsuki, S.]]	+	[[Category: Wakatsuki, S]]
	[[Category: Beta sandwich]]		[[Category: Beta sandwich]]
	[[Category: Carbohydrate binding protein]]		[[Category: Carbohydrate binding protein]]
	[[Category: Cargo receptor]]		[[Category: Cargo receptor]]
	[[Category: Protein transport]]		[[Category: Protein transport]]

OCA at 00:50, 30 September 2014

OCA — Tue, 30 Sep 2014 00:50:45 GMT

←Older revision		Revision as of 00:50, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2duq.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form==
		+	<StructureSection load='2duq' size='340' side='right' caption='[[2duq]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gv9\|1gv9]], [[1r1z\|1r1z]], [[2duo\|2duo]], [[2dup\|2dup]], [[2dur\|2dur]], [[2dus\|2dus]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LMAN2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9615 Canis lupus familiaris])</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=2duq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2duq RCSB], [http://www.ebi.ac.uk/pdbsum/2duq 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/du/2duq_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 ==
		+	VIP36 functions as a transport lectin for trafficking certain high mannose type glycoproteins in the secretory pathway. Here we report the crystal structure of VIP36 exoplasmic/luminal domain comprising a carbohydrate recognition domain and a stalk domain. The structures of VIP36 in complex with Ca(2+) and mannosyl ligands are also described. The carbohydrate recognition domain is composed of a 17-stranded antiparallel beta-sandwich and binds one Ca(2+) adjoining the carbohydrate-binding site. The structure reveals that a coordinated Ca(2+) ion orients the side chains of Asp(131), Asn(166), and His(190) for carbohydrate binding. This result explains the Ca(2+)-dependent carbohydrate binding of this protein. The Man-alpha-1,2-Man-alpha-1,2-Man, which corresponds to the D1 arm of high mannose type glycan, is recognized by eight residues through extensive hydrogen bonds. The complex structures reveal the structural basis for high mannose type glycoprotein recognition by VIP36 in a Ca(2+)-dependent and D1 arm-specific manner.

-	~~{{STRUCTURE_2duq\| PDB=2duq \| SCENE= }}~~	+	Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36.,Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S J Biol Chem. 2007 Sep 21;282(38):28246-55. Epub 2007 Jul 25. PMID:17652092<ref>PMID:17652092</ref>

-	~~===Crystal structure of VIP36 exoplasmic~~/~~lumenal domain~~, ~~Ca2+/Man-bound form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17652092}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2duq]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Canis_lupus_familiaris Canis lupus familiaris]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017652092<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Canis lupus familiaris]]		[[Category: Canis lupus familiaris]]
	[[Category: Cowieson, N P.]]		[[Category: Cowieson, N P.]]

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

OCA — Sun, 06 Jan 2013 10:10:21 GMT

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

←Older revision

Revision as of 10:10, 6 January 2013

OCA at 10:10, 6 January 2013

OCA — Sun, 06 Jan 2013 10:10:17 GMT

←Older revision		Revision as of 10:10, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2duq.png\|left\|200px]]		[[Image:2duq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2duq", 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_2duq\| PDB=2duq \| SCENE= }}		{{STRUCTURE_2duq\| PDB=2duq \| SCENE= }}

	===Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form===		===Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17652092}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17652092 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17652092}}		{{ABSTRACT_PUBMED_17652092}}

	==About this Structure==		==About this Structure==
-	~~2DUQ~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA].	+	[[2duq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17652092~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017652092</ref><references group="xtra"/>
	[[Category: Canis lupus familiaris]]		[[Category: Canis lupus familiaris]]
	[[Category: Cowieson, N P.]]		[[Category: Cowieson, N P.]]
Line 33:		Line 21:
	[[Category: Cargo receptor]]		[[Category: Cargo receptor]]
	[[Category: Protein transport]]		[[Category: Protein transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:45:00 2009''

OCA at 02:45, 18 February 2009

OCA — Wed, 18 Feb 2009 02:45:03 GMT

←Older revision		Revision as of 02:45, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2DUQ is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA].	+	2DUQ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Canis_lupus_familiaris Canis lupus familiaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUQ OCA].

	==Reference==		==Reference==
-	Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36., Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S, J Biol Chem. 2007 Sep 21;282(38):28246-55. Epub 2007 Jul 25. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17652092 17652092]~~	+	<ref group="xtra">PMID:17652092</ref><references group="xtra"/>
	[[Category: Canis lupus familiaris]]		[[Category: Canis lupus familiaris]]
-	[[Category: Single protein]]
	[[Category: Cowieson, N P.]]		[[Category: Cowieson, N P.]]
	[[Category: Kato, R.]]		[[Category: Kato, R.]]
Line 35:		Line 34:
	[[Category: Protein transport]]		[[Category: Protein transport]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 11~~:31:~~23 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:45:00 2009''

OCA at 08:31, 29 July 2008

OCA — Tue, 29 Jul 2008 08:31:24 GMT

←Older revision		Revision as of 08:31, 29 July 2008
Line 1:		Line 1:
-	[[Image:2duq.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2duq.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2duq\| PDB=2duq \| SCENE= }}		{{STRUCTURE_2duq\| PDB=2duq \| SCENE= }}

-	~~'''~~Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form~~'''~~	+	===Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man-bound form===


-	~~==Overview==~~	+	<!--
-	VIP36 functions as a transport lectin for trafficking certain high mannose type glycoproteins in the secretory pathway. Here we report the crystal structure of VIP36 exoplasmic/luminal domain comprising a carbohydrate recognition domain and a stalk domain. The structures of VIP36 in complex with Ca(2+) and mannosyl ligands are also described. The carbohydrate recognition domain is composed of a 17-~~stranded antiparallel beta~~-~~sandwich and binds one Ca(2+) adjoining the carbohydrate-binding site.~~ The ~~structure reveals that a coordinated Ca(2+) ion orients the side chains of Asp(131)~~, ~~Asn(166)~~, ~~and His~~(~~190) for carbohydrate binding~~. ~~This result explains the Ca(2+~~)~~-dependent carbohydrate binding of this protein. The Man-alpha-1~~,~~2-Man-alpha-1,2-Man, which corresponds to~~ the ~~D1 arm of high mannose type glycan, is recognized by eight residues through extensive hydrogen bonds~~. ~~The complex structures reveal the structural basis for high mannose type glycoprotein recognition by VIP36 in a Ca(2+)~~-~~dependent and D1 arm~~-~~specific manner.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17652092}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17652092 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17652092}}

	==About this Structure==		==About this Structure==
Line 30:		Line 34:
	[[Category: Cargo receptor]]		[[Category: Cargo receptor]]
	[[Category: Protein transport]]		[[Category: Protein transport]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 01~~:25:06 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:31:23 2008''