8dce - Revision history

OCA at 07:08, 21 November 2024

2024-11-21T07:08:58Z

← Older revision		Revision as of 07:08, 21 November 2024
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	The receptor binding domain (RBD) of the SARS-CoV-2 spike protein is the primary target of neutralizing antibodies and is a component of almost all current vaccines. Here, RBD immunogens were created with stabilizing amino acid changes that improve the neutralizing antibody response, as well as characteristics for production, storage, and distribution. A computational design and in vitro screening platform identified three improved immunogens, each with approximately nine amino acid changes relative to the native RBD sequence, and four key changes conserved between immunogens. The changes are adaptable to all vaccine platforms and compatible with mutations in emerging variants of concern. The immunogens elicit higher levels of neutralizing antibodies than native RBD, focus the immune response to structured neutralizing epitopes, and have increased production yields and thermostability. Incorporating these variant-independent amino acid changes in next-generation COVID vaccines may enhance the neutralizing antibody response and lead to longer duration and broader protection.		The receptor binding domain (RBD) of the SARS-CoV-2 spike protein is the primary target of neutralizing antibodies and is a component of almost all current vaccines. Here, RBD immunogens were created with stabilizing amino acid changes that improve the neutralizing antibody response, as well as characteristics for production, storage, and distribution. A computational design and in vitro screening platform identified three improved immunogens, each with approximately nine amino acid changes relative to the native RBD sequence, and four key changes conserved between immunogens. The changes are adaptable to all vaccine platforms and compatible with mutations in emerging variants of concern. The immunogens elicit higher levels of neutralizing antibodies than native RBD, focus the immune response to structured neutralizing epitopes, and have increased production yields and thermostability. Incorporating these variant-independent amino acid changes in next-generation COVID vaccines may enhance the neutralizing antibody response and lead to longer duration and broader protection.

	Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.,Dickey TH, Tang WK, Butler B, Ouahes T, Orr-Gonzalez S, Salinas ND, Lambert LE, Tolia NH Sci Adv. 2022 Sep 16;8(37):eabq8276. doi: 10.1126/sciadv.abq8276. Epub 2022 Sep, 14. PMID:36103542<ref>PMID:36103542</ref>		Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.,Dickey TH, Tang WK, Butler B, Ouahes T, Orr-Gonzalez S, Salinas ND, Lambert LE, Tolia NH Sci Adv. 2022 Sep 16;8(37):eabq8276. doi: 10.1126/sciadv.abq8276. Epub 2022 Sep , 14. PMID:36103542<ref>PMID:36103542</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[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 17:26, 18 October 2023

2023-10-18T17:26:52Z

← Older revision		Revision as of 17:26, 18 October 2023
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	==~~n/a~~==		==SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv==
	<StructureSection load='8dce' size='340' side='right'caption='[[8dce]]' scene=''>		<StructureSection load='8dce' size='340' side='right'caption='[[8dce]], [[Resolution\|resolution]] 2.00Å' 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=8DCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCE FirstGlance]. <br>		<table><tr><td colspan='2'>[[8dce]] is a 2 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=8DCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCE 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=8dce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dce OCA], [https://pdbe.org/8dce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dce RCSB], [https://www.ebi.ac.uk/pdbsum/8dce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dce 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]] 2Å</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=8dce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dce OCA], [https://pdbe.org/8dce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dce RCSB], [https://www.ebi.ac.uk/pdbsum/8dce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dce ProSAT]</span></td></tr>
	</table>		</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 receptor binding domain (RBD) of the SARS-CoV-2 spike protein is the primary target of neutralizing antibodies and is a component of almost all current vaccines. Here, RBD immunogens were created with stabilizing amino acid changes that improve the neutralizing antibody response, as well as characteristics for production, storage, and distribution. A computational design and in vitro screening platform identified three improved immunogens, each with approximately nine amino acid changes relative to the native RBD sequence, and four key changes conserved between immunogens. The changes are adaptable to all vaccine platforms and compatible with mutations in emerging variants of concern. The immunogens elicit higher levels of neutralizing antibodies than native RBD, focus the immune response to structured neutralizing epitopes, and have increased production yields and thermostability. Incorporating these variant-independent amino acid changes in next-generation COVID vaccines may enhance the neutralizing antibody response and lead to longer duration and broader protection.

			Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.,Dickey TH, Tang WK, Butler B, Ouahes T, Orr-Gonzalez S, Salinas ND, Lambert LE, Tolia NH Sci Adv. 2022 Sep 16;8(37):eabq8276. doi: 10.1126/sciadv.abq8276. Epub 2022 Sep, 14. PMID:36103542<ref>PMID:36103542</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 8dce" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Antibody 3D structures\|Antibody 3D structures]]
			*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~N/a~~]]		[[Category: Severe acute respiratory syndrome coronavirus 2]]
			[[Category: Tang WK]]
			[[Category: Tolia NH]]

OCA at 07:29, 29 June 2022

2022-06-29T07:29:42Z

← Older revision		Revision as of 07:29, 29 June 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 8dce is ~~ON HOLD~~		==n/a==
			<StructureSection load='8dce' size='340' side='right'caption='[[8dce]]' scene=''>
	~~Authors:~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCE 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=8dce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dce OCA], [https://pdbe.org/8dce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dce RCSB], [https://www.ebi.ac.uk/pdbsum/8dce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dce ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: N/a]]

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

2022-06-22T07:30:59Z

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

← Older revision	Revision as of 07:30, 22 June 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8dce is ON HOLD Authors: Description: Category: Unreleased Structures

2022-06-22T07:30:58Z

New page: '''Unreleased structure''' The entry 8dce is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8dce is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]