OCA at 11:45, 13 December 2023

OCA — Wed, 13 Dec 2023 11:45:17 GMT

←Older revision		Revision as of 11:45, 13 December 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8k45 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains==
		+	<StructureSection load='8k45' size='340' side='right'caption='[[8k45]], [[Resolution\|resolution]] 3.66Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8k45]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8K45 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8K45 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.66Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=8k45 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8k45 OCA], [https://pdbe.org/8k45 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8k45 RCSB], [https://www.ebi.ac.uk/pdbsum/8k45 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8k45 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	SARS-CoV-2 viruses are highly transmissible and immune evasive. It is critical to develop broad-spectrum prophylactic and therapeutic antibodies for potential future pandemics. Here, we used the phage display method to discover nanobodies (Nbs) for neutralizing SARS-CoV-2 viruses especially Omicron strains. The leading nanobody (Nb), namely, Nb4, with excellent physicochemical properties, can neutralize Delta and Omicron subtypes, including BA.1, BA.1.1 (BA.1 + R346K), BA.2, BA.5, BQ.1, and XBB.1. The crystal structure of Nb4 in complex with the receptor-binding domain (RBD) of BA.1 Spike protein reveals that Nb4 interacts with an epitope on the RBD overlapping with the receptor-binding motif, and thus competes with angiotensin-converting enzyme 2 (ACE2) binding. Nb4 is expected to be effective for neutralizing most recent Omicron variants, since the epitopes are evolutionarily conserved among them. Indeed, trivalent Nb4 interacts with the XBB1.5 Spike protein with low nM affinity and competes for ACE2 binding. Prophylactic and therapeutic experiments in mice indicated that Nb4 could reduce the Omicron virus loads in the lung. In particular, in prophylactic experiments, intranasal administration of multivalent Nb4 completely protected mice from Omicron infection. Taken together, these results demonstrated that Nb4 could serve as a potent and broad-spectrum prophylactic and therapeutic Nb for COVID-19.

-	~~Authors:~~ Lu, Y., ~~Gao~~, Y., ~~Yao~~, H., Xu, W., ~~Yang, H~~.	+	A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.,Yao H, Wang H, Zhang Z, Lu Y, Zhang Z, Zhang Y, Xiong X, Wang Y, Wang Z, Yang H, Zhao J, Xu W MedComm (2020). 2023 Oct 26;4(6):e397. doi: 10.1002/mco2.397. eCollection 2023 , Dec. PMID:37901798<ref>PMID:37901798</ref>

-	~~Description: A potent and broad~~-~~spectrum neutralizing nanobody for SARS~~-~~CoV-2 viruses including all major Omicron strains~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Gao, Y~~]]	+	<div class="pdbe-citations 8k45" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Yang, H~~]]	+	== References ==
-	[[Category: ~~Lu,~~ Y]]	+	<references/>
-	[[Category: ~~Yao, H~~]]	+	__TOC__
-	[[Category: Xu, W]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Vicugna pacos]]
		+	[[Category: Gao Y]]
		+	[[Category: Lu Y]]
		+	[[Category: Xu W]]
		+	[[Category: Yang H]]
		+	[[Category: Yao H]]

OCA at 07:10, 30 August 2023

OCA — Wed, 30 Aug 2023 07:10:59 GMT

←Older revision		Revision as of 07:10, 30 August 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8k45 is ON HOLD	+	The entry 8k45 is ON HOLD until Paper Publication

	Authors: Lu, Y., Gao, Y., Yao, H., Xu, W., Yang, H.		Authors: Lu, Y., Gao, Y., Yao, H., Xu, W., Yang, H.

OCA at 08:56, 2 August 2023

OCA — Wed, 02 Aug 2023 08:56:11 GMT

←Older revision		Revision as of 08:56, 2 August 2023
Line 3:		Line 3:
	The entry 8k45 is ON HOLD		The entry 8k45 is ON HOLD

-	Authors: Lu, Y., Yang, H.	+	Authors: Lu, Y., Gao, Y., Yao, H., Xu, W., Yang, H.

	Description: A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains		Description: A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Gao, Y]]
	[[Category: Yang, H]]		[[Category: Yang, H]]
	[[Category: Lu, Y]]		[[Category: Lu, Y]]
		+	[[Category: Yao, H]]
		+	[[Category: Xu, W]]

OCA: Protected "8k45" [edit=sysop:move=sysop]

OCA — Wed, 26 Jul 2023 10:49:12 GMT

Protected "8k45" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:49, 26 July 2023

OCA: New page: '''Unreleased structure''' The entry 8k45 is ON HOLD Authors: Lu, Y., Yang, H. Description: A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major...

OCA — Wed, 26 Jul 2023 10:49:11 GMT

New page: '''Unreleased structure''' The entry 8k45 is ON HOLD Authors: Lu, Y., Yang, H. Description: A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major...

New page

'''Unreleased structure'''

The entry 8k45 is ON HOLD

Authors: Lu, Y., Yang, H.

Description: A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
[[Category: Unreleased Structures]]
[[Category: Yang, H]]
[[Category: Lu, Y]]

8k45 - Revision history

OCA at 11:45, 13 December 2023

OCA at 07:10, 30 August 2023

OCA at 08:56, 2 August 2023

OCA: Protected "8k45" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8k45 is ON HOLD Authors: Lu, Y., Yang, H. Description: A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major...