OCA at 13:31, 1 February 2024

OCA — Thu, 01 Feb 2024 13:31:42 GMT

←Older revision		Revision as of 13:31, 1 February 2024
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-	====	+	==SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1==
-	<StructureSection load='7zfe' size='340' side='right'caption='[[7zfe]]' scene=''>	+	<StructureSection load='7zfe' size='340' side='right'caption='[[7zfe]], [[Resolution\|resolution]] 3.25Å' 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'>[[7zfe]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Lama_glama Lama glama] 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=7ZFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZFE 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=7zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zfe OCA], [https://pdbe.org/7zfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zfe RCSB], [https://www.ebi.ac.uk/pdbsum/7zfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zfe 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]] 3.25Å</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=7zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zfe OCA], [https://pdbe.org/7zfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zfe RCSB], [https://www.ebi.ac.uk/pdbsum/7zfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zfe 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 ==
		+	Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
		+
		+	Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.,Nutalai R, Zhou D, Tuekprakhon A, Ginn HM, Supasa P, Liu C, Huo J, Mentzer AJ, Duyvesteyn HME, Dijokaite-Guraliuc A, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Constantinides B, Webster H, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Crook D, Pollard AJ, Lambe T, Goulder P, Paterson NG, Williams MA, Hall DR, Mongkolsapaya J, Fry EE, Dejnirattisai W, Ren J, Stuart DI, Screaton GR Cell. 2022 Jun 9;185(12):2116-2131.e18. doi: 10.1016/j.cell.2022.05.014. Epub , 2022 May 20. PMID:35662412<ref>PMID:35662412</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7zfe" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Spike protein 3D structures\|Spike protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Lama glama]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Huo J]]
		+	[[Category: Ren J]]
		+	[[Category: Stuart DI]]
		+	[[Category: Zhou D]]

OCA at 05:24, 15 June 2022

OCA — Wed, 15 Jun 2022 05:24:27 GMT

←Older revision		Revision as of 05:24, 15 June 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7zfe ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7zfe' size='340' side='right'caption='[[7zfe]]' scene=''>
-	~~Authors~~: ~~Zhou, D~~.~~, Huo, J~~.~~, Ren, J~~.~~, Stuart, D~~.I.	+	== 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~~: ~~SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1~~	+	</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=7zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zfe OCA], [https://pdbe.org/7zfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zfe RCSB], [https://www.ebi.ac.uk/pdbsum/7zfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zfe ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Ren, J~~]]	+	__TOC__
-	[~~[Category~~: ~~Huo, J~~]]	+	</StructureSection>
-	[[Category: ~~Stuart, D.I~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Zhou, D~~]]	+	[[Category: Z-disk]]

OCA at 06:50, 25 May 2022

OCA — Wed, 25 May 2022 06:50:43 GMT

←Older revision		Revision as of 06:50, 25 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7zfe is ON HOLD	+	The entry 7zfe is ON HOLD until Paper Publication

	Authors: Zhou, D., Huo, J., Ren, J., Stuart, D.I.		Authors: Zhou, D., Huo, J., Ren, J., Stuart, D.I.

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

OCA — Wed, 06 Apr 2022 09:27:57 GMT

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

←Older revision

Revision as of 09:27, 6 April 2022

OCA: New page: '''Unreleased structure''' The entry 7zfe is ON HOLD Authors: Zhou, D., Huo, J., Ren, J., Stuart, D.I. Description: SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 [[...

OCA — Wed, 06 Apr 2022 09:27:56 GMT

New page: '''Unreleased structure''' The entry 7zfe is ON HOLD Authors: Zhou, D., Huo, J., Ren, J., Stuart, D.I. Description: SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 [[...

New page

'''Unreleased structure'''

The entry 7zfe is ON HOLD

Authors: Zhou, D., Huo, J., Ren, J., Stuart, D.I.

Description: SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1
[[Category: Unreleased Structures]]
[[Category: Ren, J]]
[[Category: Huo, J]]
[[Category: Stuart, D.I]]
[[Category: Zhou, D]]

7zfe - Revision history

OCA at 13:31, 1 February 2024

OCA at 05:24, 15 June 2022

OCA at 06:50, 25 May 2022

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

OCA: New page: '''Unreleased structure''' The entry 7zfe is ON HOLD Authors: Zhou, D., Huo, J., Ren, J., Stuart, D.I. Description: SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 [[...