5n11 - Revision history

OCA at 17:56, 8 November 2023

2023-11-08T17:56:15Z

←Older revision		Revision as of 17:56, 8 November 2023
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	<StructureSection load='5n11' size='340' side='right'caption='[[5n11]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5n11' size='340' side='right'caption='[[5n11]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n11]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cvhoc Cvhoc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N11 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5N11 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n11]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_coronavirus_OC43 Human coronavirus OC43]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N11 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</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]] 2.45Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31631 CVHOC])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sialate_O-acetylesterase Sialate O-acetylesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.53 3.1.1.53] </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=5n11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n11 OCA], [https://pdbe.org/5n11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n11 RCSB], [https://www.ebi.ac.uk/pdbsum/5n11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n11 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=5n11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n11 OCA], [~~http~~://pdbe.org/5n11 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n11 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n11 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n11 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q4VID6_CVHOC Q4VID6_CVHOC]] May serve as a secondary viral attachment protein for initiating infection, the spike protein being the major one. Structural protein that makes short spikes at the surface of the virus. Contains receptor binding and receptor-destroying activities. Seems to be a 'luxury' protein that is not absolutely necessary for virus infection in culture.[RuleBase:RU361278]	+	[https://www.uniprot.org/uniprot/Q4VID6_CVHOC Q4VID6_CVHOC] May serve as a secondary viral attachment protein for initiating infection, the spike protein being the major one. Structural protein that makes short spikes at the surface of the virus. Contains receptor binding and receptor-destroying activities. Seems to be a 'luxury' protein that is not absolutely necessary for virus infection in culture.[RuleBase:RU361278]
	<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: ~~Cvhoc~~]]	+	[[Category: Human coronavirus OC43]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Sialate O-acetylesterase]]~~	+	[[Category: Bakkers MJG]]
-	[[Category: Bakkers~~, M J.G~~]]	+	[[Category: Feitsma LJ]]
-	[[Category: Feitsma~~, L J]]~~	+	[[Category: Huizinga EG]]
-	~~[[Category: Groot, R J.de~~]]	+	[[Category: De Groot RJ]]
-	[[Category: Huizinga~~, E G~~]]	+
-	[[Category: ~~Coronavirus]]~~	+
-	~~[[Category: Esterase]]~~	+
-	~~[[Category: Hemagglutin]]~~	+
-	~~[[Category: Hepatitis virus]]~~	+
-	~~[[Category: Sialic acid]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 11:55, 26 August 2020

2020-08-26T11:55:20Z

←Older revision		Revision as of 11:55, 26 August 2020
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	==Crystal structure of Human beta1-coronavirus OC43 NL/A/2005 Hemagglutinin-Esterase==		==Crystal structure of Human beta1-coronavirus OC43 NL/A/2005 Hemagglutinin-Esterase==
-	<StructureSection load='5n11' size='340' side='right' caption='[[5n11]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='5n11' size='340' side='right'caption='[[5n11]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n11]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N11 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N11 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n11]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvhoc Cvhoc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N11 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5N11 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31631 CVHOC])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sialate_O-acetylesterase Sialate O-acetylesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.53 3.1.1.53] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sialate_O-acetylesterase Sialate O-acetylesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.53 3.1.1.53] </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=5n11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n11 OCA], [http://pdbe.org/5n11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n11 RCSB], [http://www.ebi.ac.uk/pdbsum/5n11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n11 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=5n11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n11 OCA], [http://pdbe.org/5n11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n11 RCSB], [http://www.ebi.ac.uk/pdbsum/5n11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n11 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5n11" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5n11" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hemagglutinin-esterase 3D structures\|Hemagglutinin-esterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cvhoc]]
		+	[[Category: Large Structures]]
	[[Category: Sialate O-acetylesterase]]		[[Category: Sialate O-acetylesterase]]
	[[Category: Bakkers, M J.G]]		[[Category: Bakkers, M J.G]]

OCA at 16:24, 22 March 2017

2017-03-22T16:24:54Z

←Older revision		Revision as of 16:24, 22 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5n11 is ~~ON HOLD~~	+	==Crystal structure of Human beta1-coronavirus OC43 NL/A/2005 Hemagglutinin-Esterase==
		+	<StructureSection load='5n11' size='340' side='right' caption='[[5n11]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5n11]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N11 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sialate_O-acetylesterase Sialate O-acetylesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.53 3.1.1.53] </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=5n11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n11 OCA], [http://pdbe.org/5n11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n11 RCSB], [http://www.ebi.ac.uk/pdbsum/5n11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n11 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q4VID6_CVHOC Q4VID6_CVHOC]] May serve as a secondary viral attachment protein for initiating infection, the spike protein being the major one. Structural protein that makes short spikes at the surface of the virus. Contains receptor binding and receptor-destroying activities. Seems to be a 'luxury' protein that is not absolutely necessary for virus infection in culture.[RuleBase:RU361278]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human beta1-coronavirus (beta1CoV) OC43 emerged relatively recently through a single zoonotic introduction. Like related animal beta1CoVs, OC43 uses 9-O-acetylated sialic acid as receptor determinant. beta1CoV receptor binding is typically controlled by attachment/fusion spike protein S and receptor-binding/receptor-destroying hemagglutinin-esterase protein HE. We show that following OC43's introduction into humans, HE-mediated receptor binding was selected against and ultimately lost through progressive accumulation of mutations in the HE lectin domain. Consequently, virion-associated receptor-destroying activity toward multivalent glycoconjugates was reduced and altered such that some clustered receptor populations are no longer cleaved. Loss of HE lectin function was also observed for another respiratory human coronavirus, HKU1. This thus appears to be an adaptation to the sialoglycome of the human respiratory tract and for replication in human airways. The findings suggest that the dynamics of virion-glycan interactions contribute to host tropism. Our observations are relevant also to other human respiratory viruses of zoonotic origin, particularly influenza A virus.

-	~~Authors:~~ Bakkers, ~~M.J.G.~~, Feitsma, ~~L.J.~~, de Groot, ~~R.J.~~, Huizinga, E.G.	+	Betacoronavirus Adaptation to Humans Involved Progressive Loss of Hemagglutinin-Esterase Lectin Activity.,Bakkers MJ, Lang Y, Feitsma LJ, Hulswit RJ, de Poot SA, van Vliet AL, Margine I, de Groot-Mijnes JD, van Kuppeveld FJ, Langereis MA, Huizinga EG, de Groot RJ Cell Host Microbe. 2017 Mar 8;21(3):356-366. doi: 10.1016/j.chom.2017.02.008. PMID:28279346<ref>PMID:28279346</ref>

-	~~Description: Crystal structure~~ of ~~Human beta1~~-~~coronavirus OC43 NL~~/A/~~2005 Hemagglutinin-Esterase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Bakkers, M.J.G]]	+	<div class="pdbe-citations 5n11" style="background-color:#fffaf0;"></div>
-	[[Category: Feitsma, L.J]]	+	== References ==
-	[[Category: Huizinga, E.G]]	+	<references/>
-	[[Category: ~~De Groot, R.J~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Sialate O-acetylesterase]]
		+	[[Category: Bakkers, M J.G]]
		+	[[Category: Feitsma, L J]]
		+	[[Category: Groot, R J.de]]
		+	[[Category: Huizinga, E G]]
		+	[[Category: Coronavirus]]
		+	[[Category: Esterase]]
		+	[[Category: Hemagglutin]]
		+	[[Category: Hepatitis virus]]
		+	[[Category: Sialic acid]]
		+	[[Category: Viral protein]]

OCA: Protected "5n11" [edit=sysop:move=sysop]

2017-03-09T11:53:50Z

Protected "5n11" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:53, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5n11 is ON HOLD Authors: Bakkers, M.J.G., Feitsma, L.J., de Groot, R.J., Huizinga, E.G. Description: Crystal structure of Human beta1-coronavirus O...

2017-03-09T11:53:49Z

New page: '''Unreleased structure''' The entry 5n11 is ON HOLD Authors: Bakkers, M.J.G., Feitsma, L.J., de Groot, R.J., Huizinga, E.G. Description: Crystal structure of Human beta1-coronavirus O...

New page

'''Unreleased structure'''

The entry 5n11 is ON HOLD

Authors: Bakkers, M.J.G., Feitsma, L.J., de Groot, R.J., Huizinga, E.G.

Description: Crystal structure of Human beta1-coronavirus OC43 NL/A/2005 Hemagglutinin-Esterase
[[Category: Unreleased Structures]]
[[Category: Bakkers, M.J.G]]
[[Category: Feitsma, L.J]]
[[Category: Huizinga, E.G]]
[[Category: De Groot, R.J]]