5yrj - Revision history

OCA at 08:36, 22 November 2023

OCA — Wed, 22 Nov 2023 08:36:03 GMT

←Older revision		Revision as of 08:36, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5yrj' size='340' side='right'caption='[[5yrj]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5yrj' size='340' side='right'caption='[[5yrj]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pteria_penguin Pteria penguin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YRJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pteria_penguin Pteria penguin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YRJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE~~+~~ION~~'>~~SO4~~</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]] 1.8Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~PCA~~:~~PYROGLUTAMIC~~+~~ACID~~'>~~PCA~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5yrj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrj OCA], [~~http~~://pdbe.org/5yrj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yrj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yrj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrj 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=5yrj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrj OCA], [https://pdbe.org/5yrj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yrj RCSB], [https://www.ebi.ac.uk/pdbsum/5yrj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B6F0T7_PTEPN B6F0T7_PTEPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Pteria penguin]]		[[Category: Pteria penguin]]
-	[[Category: Nakae, S]]	+	[[Category: Nakae S]]
-	[[Category: Ogawa, T]]	+	[[Category: Ogawa T]]
-	[[Category: Shionyu, M]]	+	[[Category: Shionyu M]]
-	[[Category: Shirai, T]]	+	[[Category: Shirai T]]
-	~~[[Category: Biomineralization]]~~	+
-	~~[[Category: Calcite]]~~	+
-	~~[[Category: Docking simulation]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Post-translational modification]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 09:26, 21 October 2020

OCA — Wed, 21 Oct 2020 09:26:15 GMT

←Older revision		Revision as of 09:26, 21 October 2020
Line 1:		Line 1:

	==PPL3B-isomaltose complex==		==PPL3B-isomaltose complex==
-	<StructureSection load='5yrj' size='340' side='right' caption='[[5yrj]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5yrj' size='340' side='right'caption='[[5yrj]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yrj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pteria_penguin Pteria penguin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YRJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yrj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pteria_penguin Pteria penguin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YRJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=5yrj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrj OCA], [http://pdbe.org/5yrj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrj RCSB], [http://www.ebi.ac.uk/pdbsum/5yrj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrj ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yrj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrj OCA], [http://pdbe.org/5yrj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrj RCSB], [http://www.ebi.ac.uk/pdbsum/5yrj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pteria penguin]]		[[Category: Pteria penguin]]
	[[Category: Nakae, S]]		[[Category: Nakae, S]]

OCA at 07:19, 29 August 2018

OCA — Wed, 29 Aug 2018 07:19:45 GMT

←Older revision		Revision as of 07:19, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yrj is ~~ON HOLD until Paper~~ Publication	+	==PPL3B-isomaltose complex==
		+	<StructureSection load='5yrj' size='340' side='right' caption='[[5yrj]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yrj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pteria_penguin Pteria penguin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YRJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=5yrj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrj OCA], [http://pdbe.org/5yrj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yrj RCSB], [http://www.ebi.ac.uk/pdbsum/5yrj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrj ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nacreous layer of pearl oysters is one of the major biominerals of commercial and industrial interest. Jacalin-related lectins, including PPL3 isoforms, are known to regulate biomineralization of the Pteria penguin pearl shell, although the molecular mechanisms are largely unknown. The PPL3 crystal structures were determined partly by utilizing microgravity environments for 3 isoforms, namely, PPL3A, PPL3B, and PPL3C. The structures revealed a tail-to-tail dimer structure established by forming a unique inter-subunit disulfide bond at C-termini. The N-terminal residues were found in pyroglutamate form, and this was partly explained by the post-translational modification of PPL3 isoforms implied from the discrepancy between amino acid and gene sequences. The complex structures with trehalose and isomaltose indicated that the novel specificity originated from the unique alpha-helix of PPL3 isoforms. Docking simulations of PPL3B to various calcite crystal faces suggested the edge of a beta-sheet and the carbohydrate-binding site rich in charged residues were the interface to the biomineral, and implied that the isoforms differed in calcite interactions.

-	~~Authors: Nakae~~, S., Shionyu, M., Ogawa, T., Shirai, T.	+	Structures of jacalin-related lectin PPL3 regulating pearl shell biomineralization.,Nakae S, Shionyu M, Ogawa T, Shirai T Proteins. 2018 Jun;86(6):644-653. doi: 10.1002/prot.25491. Epub 2018 Mar 23. PMID:29524263<ref>PMID:29524263</ref>

-	~~Description: PPL3B-isomaltose complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Shionyu, M~~]]	+	<div class="pdbe-citations 5yrj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pteria penguin]]
	[[Category: Nakae, S]]		[[Category: Nakae, S]]
	[[Category: Ogawa, T]]		[[Category: Ogawa, T]]
		+	[[Category: Shionyu, M]]
	[[Category: Shirai, T]]		[[Category: Shirai, T]]
		+	[[Category: Biomineralization]]
		+	[[Category: Calcite]]
		+	[[Category: Docking simulation]]
		+	[[Category: Lectin]]
		+	[[Category: Post-translational modification]]
		+	[[Category: Sugar binding protein]]

OCA at 04:56, 29 November 2017

OCA — Wed, 29 Nov 2017 04:56:11 GMT

←Older revision		Revision as of 04:56, 29 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yrj is ON HOLD	+	The entry 5yrj is ON HOLD until Paper Publication

	Authors: Nakae, S., Shionyu, M., Ogawa, T., Shirai, T.		Authors: Nakae, S., Shionyu, M., Ogawa, T., Shirai, T.

OCA: Protected "5yrj" [edit=sysop:move=sysop]

OCA — Wed, 15 Nov 2017 06:18:01 GMT

Protected "5yrj" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:18, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yrj is ON HOLD Authors: Nakae, S., Shionyu, M., Ogawa, T., Shirai, T. Description: PPL3B-isomaltose complex Category: Unreleased Structures [[...

OCA — Wed, 15 Nov 2017 06:18:00 GMT

New page: '''Unreleased structure''' The entry 5yrj is ON HOLD Authors: Nakae, S., Shionyu, M., Ogawa, T., Shirai, T. Description: PPL3B-isomaltose complex Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 5yrj is ON HOLD

Authors: Nakae, S., Shionyu, M., Ogawa, T., Shirai, T.

Description: PPL3B-isomaltose complex
[[Category: Unreleased Structures]]
[[Category: Shionyu, M]]
[[Category: Nakae, S]]
[[Category: Ogawa, T]]
[[Category: Shirai, T]]