8gpy - Revision history

OCA at 15:03, 13 March 2024

2024-03-13T15:03:13Z

←Older revision		Revision as of 15:03, 13 March 2024
Line 9:		Line 9:
	== Function ==		== 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]		[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 ==
-	The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT(50) values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.
-
-	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.,Guo Y, Zhang G, Yang Q, Xie X, Lu Y, Cheng X, Wang H, Liang J, Tang J, Gao Y, Shang H, Dai J, Shi Y, Zhou J, Zhou J, Guo H, Yang H, Qi J, Liu L, Ma S, Zhang B, Huo Q, Xie Y, Wu J, Dong F, Zhang S, Lou Z, Gao Y, Song Z, Wang W, Sun Z, Yang X, Xiong D, Liu F, Chen X, Zhu P, Wang X, Cheng T, Rao Z Nat Commun. 2023 Jun 15;14(1):3537. doi: 10.1038/s41467-023-39267-x. PMID:37322000<ref>PMID:37322000</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8gpy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]		*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
		+	*[[Spike protein 3D structures\|Spike protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:13, 29 November 2023

2023-11-29T18:13:38Z

←Older revision		Revision as of 18:13, 29 November 2023
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 8gpy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 8gpy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:19, 28 June 2023

2023-06-28T21:19:56Z

←Older revision		Revision as of 21:19, 28 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8gpy is ~~ON HOLD~~	+	==Crystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv==
		+	<StructureSection load='8gpy' size='340' side='right'caption='[[8gpy]], [[Resolution\|resolution]] 2.51Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8gpy]] is a 6 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=8GPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GPY FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.51Å</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=8gpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gpy OCA], [https://pdbe.org/8gpy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gpy RCSB], [https://www.ebi.ac.uk/pdbsum/8gpy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gpy 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 ==
		+	The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT(50) values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.

-	~~Authors: Gao~~, Y.X., Song, Z.D., Wang, W.M.~~, Guo, Y~~.	+	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.,Guo Y, Zhang G, Yang Q, Xie X, Lu Y, Cheng X, Wang H, Liang J, Tang J, Gao Y, Shang H, Dai J, Shi Y, Zhou J, Zhou J, Guo H, Yang H, Qi J, Liu L, Ma S, Zhang B, Huo Q, Xie Y, Wu J, Dong F, Zhang S, Lou Z, Gao Y, Song Z, Wang W, Sun Z, Yang X, Xiong D, Liu F, Chen X, Zhu P, Wang X, Cheng T, Rao Z Nat Commun. 2023 Jun 15;14(1):3537. doi: 10.1038/s41467-023-39267-x. PMID:37322000<ref>PMID:37322000</ref>

-	~~Description: Crystal structure~~ of ~~Omicron BA~~.4/~~5 RBD in complex with a neutralizing antibody scFv~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Wang, W.M~~]]	+	<div class="pdbe-citations 8gpy" style="background-color:#fffaf0;"></div>
-	[[Category: Guo, Y]]	+	== References ==
-	[[Category: Song~~, Z.D~~]]	+	<references/>
-	[[Category: ~~Gao, Y.X~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Gao YX]]
		+	[[Category: Guo Y]]
		+	[[Category: Song ZD]]
		+	[[Category: Wang WM]]

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

2022-09-07T15:39:47Z

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

←Older revision

Revision as of 15:39, 7 September 2022

OCA: New page: '''Unreleased structure''' The entry 8gpy is ON HOLD Authors: Gao, Y.X., Song, Z.D., Wang, W.M., Guo, Y. Description: Crystal structure of Omicron BA.4/5 RBD in complex with a neutrali...

2022-09-07T15:39:46Z

New page: '''Unreleased structure''' The entry 8gpy is ON HOLD Authors: Gao, Y.X., Song, Z.D., Wang, W.M., Guo, Y. Description: Crystal structure of Omicron BA.4/5 RBD in complex with a neutrali...

New page

'''Unreleased structure'''

The entry 8gpy is ON HOLD

Authors: Gao, Y.X., Song, Z.D., Wang, W.M., Guo, Y.

Description: Crystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv
[[Category: Unreleased Structures]]
[[Category: Wang, W.M]]
[[Category: Guo, Y]]
[[Category: Song, Z.D]]
[[Category: Gao, Y.X]]