5xqp - Revision history

OCA at 08:10, 22 November 2023

OCA — Wed, 22 Nov 2023 08:10:33 GMT

←Older revision		Revision as of 08:10, 22 November 2023
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	<StructureSection load='5xqp' size='340' side='right'caption='[[5xqp]], [[Resolution\|resolution]] 1.00Å' scene=''>		<StructureSection load='5xqp' size='340' side='right'caption='[[5xqp]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xqp]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Enchelyopus_elongatus Enchelyopus~~ elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xqp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoarces_elongatus Zoarces elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XQP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1Å</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=5xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqp OCA], [~~http~~://pdbe.org/5xqp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xqp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xqp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqp ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=5xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqp OCA], [https://pdbe.org/5xqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xqp RCSB], [https://www.ebi.ac.uk/pdbsum/5xqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q53UJ4_9TELE Q53UJ4_9TELE]] Lowers the blood freezing point. Contributes to protect fish blood from freezing at subzero sea water temperatures. Binds to nascent ice crystals and prevents further growth.[RuleBase:RU362061]	+	[https://www.uniprot.org/uniprot/Q53UJ4_9TELE Q53UJ4_9TELE] Lowers the blood freezing point. Contributes to protect fish blood from freezing at subzero sea water temperatures. Binds to nascent ice crystals and prevents further growth.[RuleBase:RU362061]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Enchelyopus elongatus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adachi, M]]	+	[[Category: Zoarces elongatus]]
-	[[Category: Kondo, H]]	+	[[Category: Adachi M]]
-	[[Category: Shibazaki, C]]	+	[[Category: Kondo H]]
-	[[Category: Shimizu, R]]	+	[[Category: Shibazaki C]]
-	[[Category: Tsuda, S]]	+	[[Category: Shimizu R]]
-	~~[[Category: Antifreeze protein~~]]	+	[[Category: Tsuda S]]

OCA at 06:57, 14 October 2020

OCA — Wed, 14 Oct 2020 06:57:03 GMT

←Older revision		Revision as of 06:57, 14 October 2020
Line 1:		Line 1:

	==Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121 form==		==Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121 form==
-	<StructureSection load='5xqp' size='340' side='right' caption='[[5xqp]], [[Resolution\|resolution]] 1.00Å' scene=''>	+	<StructureSection load='5xqp' size='340' side='right'caption='[[5xqp]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xqp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enchelyopus_elongatus Enchelyopus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xqp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enchelyopus_elongatus Enchelyopus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XQP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</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=5xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqp OCA], [http://pdbe.org/5xqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqp RCSB], [http://www.ebi.ac.uk/pdbsum/5xqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqp 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=5xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqp OCA], [http://pdbe.org/5xqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqp RCSB], [http://www.ebi.ac.uk/pdbsum/5xqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5xqp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xqp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antifreeze protein 3D structures\|Antifreeze protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Enchelyopus elongatus]]		[[Category: Enchelyopus elongatus]]
		+	[[Category: Large Structures]]
	[[Category: Adachi, M]]		[[Category: Adachi, M]]
	[[Category: Kondo, H]]		[[Category: Kondo, H]]

OCA at 07:41, 23 May 2018

OCA — Wed, 23 May 2018 07:41:53 GMT

←Older revision		Revision as of 07:41, 23 May 2018
Line 3:		Line 3:
	<StructureSection load='5xqp' size='340' side='right' caption='[[5xqp]], [[Resolution\|resolution]] 1.00Å' scene=''>		<StructureSection load='5xqp' size='340' side='right' caption='[[5xqp]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xqp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xqp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enchelyopus_elongatus Enchelyopus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqp OCA], [http://pdbe.org/5xqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqp RCSB], [http://www.ebi.ac.uk/pdbsum/5xqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqp ProSAT]</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=5xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqp OCA], [http://pdbe.org/5xqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqp RCSB], [http://www.ebi.ac.uk/pdbsum/5xqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqp ProSAT]</span></td></tr>
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q53UJ4_9TELE Q53UJ4_9TELE]] Lowers the blood freezing point. Contributes to protect fish blood from freezing at subzero sea water temperatures. Binds to nascent ice crystals and prevents further growth.[RuleBase:RU362061]		[[http://www.uniprot.org/uniprot/Q53UJ4_9TELE Q53UJ4_9TELE]] Lowers the blood freezing point. Contributes to protect fish blood from freezing at subzero sea water temperatures. Binds to nascent ice crystals and prevents further growth.[RuleBase:RU362061]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of approximately 50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the [Formula: see text] first prism plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the [Formula: see text] pyramidal ice plane. The order of ice-binding strength was A20L < A20G < WT < A20T < A20V < A20I, where the top three mutants capable of binding to the first prism and the pyramidal ice planes commonly contained a bifurcated gamma-CH3 group. These results suggest that a fine-tuning of the surface of Zoarcidae-derived IBP assisted by a side-chain group regulates the holding property of its polypentagonal water network, the function of which is to freeze the host protein to specific ice planes.
		+
		+	Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein.,Mahatabuddin S, Fukami D, Arai T, Nishimiya Y, Shimizu R, Shibazaki C, Kondo H, Adachi M, Tsuda S Proc Natl Acad Sci U S A. 2018 May 7. pii: 1800635115. doi:, 10.1073/pnas.1800635115. PMID:29735675<ref>PMID:29735675</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xqp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enchelyopus elongatus]]
	[[Category: Adachi, M]]		[[Category: Adachi, M]]
	[[Category: Kondo, H]]		[[Category: Kondo, H]]

OCA at 05:26, 16 May 2018

OCA — Wed, 16 May 2018 05:26:12 GMT

←Older revision		Revision as of 05:26, 16 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5xqp is ON HOLD until Paper Publication~~	+	==Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121 form==
-		+	<StructureSection load='5xqp' size='340' side='right' caption='[[5xqp]], [[Resolution\|resolution]] 1.00Å' scene=''>
-	~~Authors: Adachi, M., Shimizu, R., Shibazaki, C., Kondo, H., Tsuda, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xqp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQP FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121 form	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqp OCA], [http://pdbe.org/5xqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqp RCSB], [http://www.ebi.ac.uk/pdbsum/5xqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q53UJ4_9TELE Q53UJ4_9TELE]] Lowers the blood freezing point. Contributes to protect fish blood from freezing at subzero sea water temperatures. Binds to nascent ice crystals and prevents further growth.[RuleBase:RU362061]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Adachi, M]]
	[[Category: Kondo, H]]		[[Category: Kondo, H]]
	[[Category: Shibazaki, C]]		[[Category: Shibazaki, C]]
		+	[[Category: Shimizu, R]]
	[[Category: Tsuda, S]]		[[Category: Tsuda, S]]
-	[[Category: ~~Shimizu, R]]~~	+	[[Category: Antifreeze protein]]
-	~~[[Category: Adachi, M~~]]	+

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

OCA — Wed, 27 Sep 2017 15:41:21 GMT

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

←Older revision

Revision as of 15:41, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xqp is ON HOLD until Paper Publication Authors: Adachi, M., Shimizu, R., Shibazaki, C., Kondo, H., Tsuda, S. Description: Crystal structure of Not...

OCA — Wed, 27 Sep 2017 15:41:20 GMT

New page: '''Unreleased structure''' The entry 5xqp is ON HOLD until Paper Publication Authors: Adachi, M., Shimizu, R., Shibazaki, C., Kondo, H., Tsuda, S. Description: Crystal structure of Not...

New page

'''Unreleased structure'''

The entry 5xqp is ON HOLD until Paper Publication

Authors: Adachi, M., Shimizu, R., Shibazaki, C., Kondo, H., Tsuda, S.

Description: Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121 form
[[Category: Unreleased Structures]]
[[Category: Kondo, H]]
[[Category: Shibazaki, C]]
[[Category: Tsuda, S]]
[[Category: Shimizu, R]]
[[Category: Adachi, M]]