4lej - Revision history

OCA at 12:19, 1 March 2024

OCA — Fri, 01 Mar 2024 12:19:17 GMT

←Older revision		Revision as of 12:19, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.402Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4lej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lej OCA], [https://pdbe.org/4lej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lej RCSB], [https://www.ebi.ac.uk/pdbsum/4lej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lej 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=4lej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lej OCA], [https://pdbe.org/4lej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lej RCSB], [https://www.ebi.ac.uk/pdbsum/4lej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lej ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/VCL_PINKO VCL_PINKO] Seed storage protein.<ref>PMID:18084088</ref> <ref>PMID:18690685</ref>		[https://www.uniprot.org/uniprot/VCL_PINKO VCL_PINKO] Seed storage protein.<ref>PMID:18084088</ref> <ref>PMID:18690685</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The prevalence of food allergy has increased in recent years, and Korean pine vicilin is a potential food allergen. We have previously reported the crystallization of Korean pine vicilin purified from raw pine nut. Here we report the isolation of vicilin mRNA and the crystal structure of Korean pine vicilin at 2.40 A resolution. The overall structure of pine nut vicilin is similar to the structures of other 7S seed storage proteins and consists of an N-terminal domain and a C-terminal domain. Each assumes a cupin fold, and they are symmetrically related about a pseudodyad axis. Three vicilin molecules form a doughnut-shaped trimer through head-to-tail association. Structure characterization of Korean pine nut vicilin unexpectedly showed that, in its native trimeric state, the vicilin has three copper ligands. Sequence alignments suggested that the copper-coordinating residues were conserved in winter squash, sesame, tomato, and several tree nuts, while they were not conserved in a number of legumes, including peanut and soybean. Additional studies are needed to assess whether the copper-coordinating property of vicilins has a biological function in the relevant plants. The nutritional value of this copper-coordinating protein in tree nuts and other edible seeds may be worth further investigations.
-
-	Crystal Structure of Korean Pine ( Pinus koraiensis ) 7S Seed Storage Protein with Copper Ligands.,Jin T, Wang Y, Chen YW, Fu TJ, Kothary MH, McHugh TH, Zhang Y J Agric Food Chem. 2013 Dec 23. PMID:24328105<ref>PMID:24328105</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4lej" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:56, 14 December 2022

OCA — Wed, 14 Dec 2022 10:56:16 GMT

←Older revision		Revision as of 10:56, 14 December 2022
Line 3:		Line 3:
	<StructureSection load='4lej' size='340' side='right'caption='[[4lej]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4lej' size='340' side='right'caption='[[4lej]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4lej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lej OCA], [~~http~~://pdbe.org/4lej PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4lej RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4lej PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4lej 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=4lej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lej OCA], [https://pdbe.org/4lej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lej RCSB], [https://www.ebi.ac.uk/pdbsum/4lej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lej ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/VCL_PINKO VCL_PINKO] Seed storage protein.<ref>PMID:18084088</ref> <ref>PMID:18690685</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Pinus koraiensis]]		[[Category: Pinus koraiensis]]
-	[[Category: Jin~~, T C~~]]	+	[[Category: Jin TC]]
-	[[Category: Wang, Y]]	+	[[Category: Wang Y]]
-	[[Category: Zhang~~, Y Z]]~~	+	[[Category: Zhang YZ]]
-	~~[[Category: Allergen]]~~	+
-	~~[[Category: Cupin]]~~	+
-	~~[[Category: Plant protein]]~~	+
-	~~[[Category: Seed storage]]~~	+
-	~~[[Category: Seed storage protein~~]]	+

OCA at 04:56, 13 February 2020

OCA — Thu, 13 Feb 2020 04:56:00 GMT

←Older revision		Revision as of 04:56, 13 February 2020
Line 1:		Line 1:

	==Crystal Structure of the Korean pine (Pinus koraiensis) vicilin==		==Crystal Structure of the Korean pine (Pinus koraiensis) vicilin==
-	<StructureSection load='4lej' size='340' side='right' caption='[[4lej]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4lej' size='340' side='right'caption='[[4lej]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pinus koraiensis]]		[[Category: Pinus koraiensis]]
	[[Category: Jin, T C]]		[[Category: Jin, T C]]

OCA at 13:17, 11 August 2016

OCA — Thu, 11 Aug 2016 13:17:23 GMT

←Older revision		Revision as of 13:17, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the Korean pine (Pinus koraiensis) vicilin==		==Crystal Structure of the Korean pine (Pinus koraiensis) vicilin==
	<StructureSection load='4lej' size='340' side='right' caption='[[4lej]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4lej' size='340' side='right' caption='[[4lej]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4lej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lej OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lej RCSB], [http://www.ebi.ac.uk/pdbsum/4lej 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=4lej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lej OCA], [http://pdbe.org/4lej PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lej RCSB], [http://www.ebi.ac.uk/pdbsum/4lej PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lej ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4lej" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:27, 22 January 2015

OCA — Thu, 22 Jan 2015 06:27:18 GMT

←Older revision		Revision as of 06:27, 22 January 2015
Line 19:		Line 19:
	</StructureSection>		</StructureSection>
	[[Category: Pinus koraiensis]]		[[Category: Pinus koraiensis]]
-	[[Category: Jin, T C.]]	+	[[Category: Jin, T C]]
-	[[Category: Wang, Y.]]	+	[[Category: Wang, Y]]
-	[[Category: Zhang, Y Z.]]	+	[[Category: Zhang, Y Z]]
	[[Category: Allergen]]		[[Category: Allergen]]
	[[Category: Cupin]]		[[Category: Cupin]]

OCA at 08:28, 20 October 2014

OCA — Mon, 20 Oct 2014 08:28:45 GMT

←Older revision		Revision as of 08:28, 20 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4lej\| PDB=4lej \| SCENE= }}~~	+	==Crystal Structure of the Korean pine (Pinus koraiensis) vicilin==
-	===Crystal Structure of the Korean pine (Pinus koraiensis) vicilin===	+	<StructureSection load='4lej' size='340' side='right' caption='[[4lej]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24328105}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4lej]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LEJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4lej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lej OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lej RCSB], [http://www.ebi.ac.uk/pdbsum/4lej PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The prevalence of food allergy has increased in recent years, and Korean pine vicilin is a potential food allergen. We have previously reported the crystallization of Korean pine vicilin purified from raw pine nut. Here we report the isolation of vicilin mRNA and the crystal structure of Korean pine vicilin at 2.40 A resolution. The overall structure of pine nut vicilin is similar to the structures of other 7S seed storage proteins and consists of an N-terminal domain and a C-terminal domain. Each assumes a cupin fold, and they are symmetrically related about a pseudodyad axis. Three vicilin molecules form a doughnut-shaped trimer through head-to-tail association. Structure characterization of Korean pine nut vicilin unexpectedly showed that, in its native trimeric state, the vicilin has three copper ligands. Sequence alignments suggested that the copper-coordinating residues were conserved in winter squash, sesame, tomato, and several tree nuts, while they were not conserved in a number of legumes, including peanut and soybean. Additional studies are needed to assess whether the copper-coordinating property of vicilins has a biological function in the relevant plants. The nutritional value of this copper-coordinating protein in tree nuts and other edible seeds may be worth further investigations.

-	~~==About this~~ Structure==	+	Crystal Structure of Korean Pine ( Pinus koraiensis ) 7S Seed Storage Protein with Copper Ligands.,Jin T, Wang Y, Chen YW, Fu TJ, Kothary MH, McHugh TH, Zhang Y J Agric Food Chem. 2013 Dec 23. PMID:24328105<ref>PMID:24328105</ref>
-	~~[[4lej]] is a 1 chain structure~~ with ~~sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pinus_koraiensis Pinus koraiensis]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024328105</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Pinus koraiensis]]		[[Category: Pinus koraiensis]]
	[[Category: Jin, T C.]]		[[Category: Jin, T C.]]

OCA at 06:54, 22 January 2014

OCA — Wed, 22 Jan 2014 06:54:40 GMT

←Older revision		Revision as of 06:54, 22 January 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4lej\| PDB=4lej \| SCENE= }}
		+	===Crystal Structure of the Korean pine (Pinus koraiensis) vicilin===
		+	{{ABSTRACT_PUBMED_24328105}}

-	~~The entry~~ 4lej is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4lej]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pinus_koraiensis Pinus koraiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LEJ OCA].

-	~~Authors~~: Jin, T.C., Wang, Y., Zhang, Y.Z.	+	==Reference==
-		+	<ref group="xtra">PMID:024328105</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal Structure of the Korean pine (Pinus koraiensis) vicilin~~	+	[[Category: Pinus koraiensis]]
		+	[[Category: Jin, T C.]]
		+	[[Category: Wang, Y.]]
		+	[[Category: Zhang, Y Z.]]
		+	[[Category: Allergen]]
		+	[[Category: Cupin]]
		+	[[Category: Plant protein]]
		+	[[Category: Seed storage]]
		+	[[Category: Seed storage protein]]

OCA at 07:34, 15 January 2014

OCA — Wed, 15 Jan 2014 07:34:01 GMT

←Older revision		Revision as of 07:34, 15 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4lej is ON HOLD	+	The entry 4lej is ON HOLD until Paper Publication

	Authors: Jin, T.C., Wang, Y., Zhang, Y.Z.		Authors: Jin, T.C., Wang, Y., Zhang, Y.Z.

	Description: Crystal Structure of the Korean pine (Pinus koraiensis) vicilin		Description: Crystal Structure of the Korean pine (Pinus koraiensis) vicilin

OCA: Protected "4lej" [edit=sysop:move=sysop]

OCA — Wed, 03 Jul 2013 13:27:04 GMT

Protected "4lej" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:27, 3 July 2013

OCA: New page: '''Unreleased structure''' The entry 4lej is ON HOLD Authors: Jin, T.C., Wang, Y., Zhang, Y.Z. Description: Crystal Structure of the Korean pine (Pinus koraiensis) vicilin

OCA — Wed, 03 Jul 2013 13:27:03 GMT

New page: '''Unreleased structure''' The entry 4lej is ON HOLD Authors: Jin, T.C., Wang, Y., Zhang, Y.Z. Description: Crystal Structure of the Korean pine (Pinus koraiensis) vicilin

New page

'''Unreleased structure'''

The entry 4lej is ON HOLD

Authors: Jin, T.C., Wang, Y., Zhang, Y.Z.

Description: Crystal Structure of the Korean pine (Pinus koraiensis) vicilin