7u0n - Revision history

OCA at 17:09, 18 October 2023

OCA — Wed, 18 Oct 2023 17:09:58 GMT

←Older revision		Revision as of 17:09, 18 October 2023
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	==Crystal structure of chimeric omicron RBD (strain BA.1) complexed with human ACE2==		==Crystal structure of chimeric omicron RBD (strain BA.1) complexed with human ACE2==
-	<StructureSection load='7u0n' size='340' side='right'caption='[[7u0n]]' scene=''>	+	<StructureSection load='7u0n' size='340' side='right'caption='[[7u0n]], [[Resolution\|resolution]] 2.61Å' 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=7U0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7u0n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7U0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0N 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=7u0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0n OCA], [https://pdbe.org/7u0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0n RCSB], [https://www.ebi.ac.uk/pdbsum/7u0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0n 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]] 2.61Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7u0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0n OCA], [https://pdbe.org/7u0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0n RCSB], [https://www.ebi.ac.uk/pdbsum/7u0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0n ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ACE2_HUMAN ACE2_HUMAN] Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin-13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. In case of human coronaviruses SARS and HCoV-NL63 infections, serve as functional receptor for the spike glycoprotein of both coronaviruses.<ref>PMID:10969042</ref> <ref>PMID:10924499</ref> <ref>PMID:14647384</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The highly contagious and fast-spreading omicron variant of SARS-CoV-2 infects the respiratory tracts efficiently. The receptor-binding domain (RBD) of the omicron spike protein recognizes human angiotensin-converting enzyme 2 (ACE2) as its receptor and plays a critical role in the tissue tropism of SARS-CoV-2. Here, we showed that the omicron RBD (strain BA.1) binds to ACE2 more strongly than does the prototypic RBD from the original Wuhan strain. We also measured how individual omicron mutations affect ACE2 binding. We further determined the crystal structure of the omicron RBD (engineered to facilitate crystallization) complexed with ACE2 at 2.6 A. The structure shows that omicron mutations caused significant structural rearrangements of two mutational hot spots at the RBD/ACE2 interface, elucidating how each omicron mutation affects ACE2 binding. The enhanced ACE2 binding by the omicron RBD may facilitate the omicron variant's infection of the respiratory tracts where ACE2 expression level is low. Our study provides insights into the receptor recognition and tissue tropism of the omicron variant. IMPORTANCE Despite the scarcity of the SARS-CoV-2 receptor-human angiotensin-converting enzyme 2 (ACE2)-in the respiratory tract, the omicron variant efficiently infects the respiratory tract, causing rapid and widespread infections of COVID-19. The omicron variant contains extensive mutations in the receptor-binding domain (RBD) of its spike protein that recognizes human ACE2. Here, using a combination of biochemical and X-ray crystallographic approaches, we showed that the omicron RBD binds to ACE2 with enhanced affinity and also elucidated the role of each of the omicron mutations in ACE2 binding. The enhanced ACE2 binding by the omicron RBD may contribute to the omicron variant's new viral tropism in the respiratory tract despite the low level of ACE2 expression in the tissue. These findings help us to understand tissue tropism of the omicron variant and shed light on the molecular evolution of SARS-CoV-2.
		+
		+	Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA.1.,Geng Q, Shi K, Ye G, Zhang W, Aihara H, Li F J Virol. 2022 Apr 27;96(8):e0024922. doi: 10.1128/jvi.00249-22. Epub 2022 Mar 28. PMID:35343765<ref>PMID:35343765</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7u0n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Angiotensin-Converting Enzyme 3D structures\|Angiotensin-Converting Enzyme 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
	[[Category: Aihara H]]		[[Category: Aihara H]]
	[[Category: Geng Q]]		[[Category: Geng Q]]

OCA at 14:52, 31 August 2022

OCA — Wed, 31 Aug 2022 14:52:28 GMT

←Older revision		Revision as of 14:52, 31 August 2022
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-	====	+	==Crystal structure of chimeric omicron RBD (strain BA.1) complexed with human ACE2==
	<StructureSection load='7u0n' size='340' side='right'caption='[[7u0n]]' scene=''>		<StructureSection load='7u0n' size='340' side='right'caption='[[7u0n]]' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7U0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0N 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=7u0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0n OCA], [https://pdbe.org/7u0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0n RCSB], [https://www.ebi.ac.uk/pdbsum/7u0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0n ProSAT]</span></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=7u0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0n OCA], [https://pdbe.org/7u0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0n RCSB], [https://www.ebi.ac.uk/pdbsum/7u0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0n ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Aihara H]]
		+	[[Category: Geng Q]]
		+	[[Category: Li F]]
		+	[[Category: Shi K]]
		+	[[Category: Ye G]]
		+	[[Category: Zhang W]]

OCA at 10:48, 30 March 2022

OCA — Wed, 30 Mar 2022 10:48:24 GMT

←Older revision		Revision as of 10:48, 30 March 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7u0n ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7u0n' size='340' side='right'caption='[[7u0n]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7u0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0n OCA], [https://pdbe.org/7u0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0n RCSB], [https://www.ebi.ac.uk/pdbsum/7u0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0n ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 04:54, 9 March 2022

OCA — Wed, 09 Mar 2022 04:54:36 GMT

←Older revision		Revision as of 04:54, 9 March 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7u0n is ON HOLD ~~until sometime in the future~~	+	The entry 7u0n is ON HOLD

	Authors:		Authors:

OCA: Protected "7u0n" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2022 05:06:24 GMT

Protected "7u0n" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:06, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7u0n is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Mar 2022 05:06:23 GMT

New page: '''Unreleased structure''' The entry 7u0n is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7u0n is ON HOLD until sometime in the future

Authors:

Description:
[[Category: Unreleased Structures]]