OCA at 07:05, 25 October 2023

OCA — Wed, 25 Oct 2023 07:05:28 GMT

←Older revision		Revision as of 07:05, 25 October 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8hgm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11==
		+	<StructureSection load='8hgm' size='340' side='right'caption='[[8hgm]], [[Resolution\|resolution]] 3.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8hgm]] is a 3 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=8HGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8HGM 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]] 3.4Å</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=8hgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8hgm OCA], [https://pdbe.org/8hgm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8hgm RCSB], [https://www.ebi.ac.uk/pdbsum/8hgm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8hgm 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 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.

-	~~Authors: Moriyama~~, S., Anraku, Y~~., Muranishi~~, S., Adachi, Y., Kuroda, D., Higuchi, Y., Kotaki, R., Tonouchi, K., Yumoto, K., Suzuki, T~~., Kita, S.~~, Fukuhara, H., Kuroda, Y., Yamamoto, T., Onodera, T., Fukushi, S., Maeda, K., Nakamura-Uchiyama, F., Hashiguchi, T., Hoshino, A., Maenaka, K., Takahashi, Y.	+	Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.,Moriyama S, Anraku Y, Taminishi S, Adachi Y, Kuroda D, Kita S, Higuchi Y, Kirita Y, Kotaki R, Tonouchi K, Yumoto K, Suzuki T, Someya T, Fukuhara H, Kuroda Y, Yamamoto T, Onodera T, Fukushi S, Maeda K, Nakamura-Uchiyama F, Hashiguchi T, Hoshino A, Maenaka K, Takahashi Y Nat Commun. 2023 Jul 14;14(1):4198. doi: 10.1038/s41467-023-39890-8. PMID:37452031<ref>PMID:37452031</ref>

-	~~Description: Structure~~ of ~~SARS~~-~~CoV~~-~~2 spike RBD in complex with neutralizing antibody NIV-11~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Yamamoto, T~~]]	+	<div class="pdbe-citations 8hgm" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Fukuhara, H~~]]	+	== References ==
-	[[Category: ~~Kuroda,~~ Y]]	+	<references/>
-	[[Category: ~~Hoshino, A~~]]	+	__TOC__
-	[[Category: ~~Kotaki, R~~]]	+	</StructureSection>
-	[[Category: ~~Moriyama,~~ S]]	+	[[Category: Homo sapiens]]
-	[[Category: Higuchi, Y]]	+	[[Category: Large Structures]]
-	[[Category: ~~Fukushi, S~~]]	+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
-	[[Category: ~~Takahashi, Y~~]]	+	[[Category: Adachi Y]]
-	[[Category: ~~Maenaka, K~~]]	+	[[Category: Anraku Y]]
-	[[Category: ~~Nakamura-Uchiyama, F~~]]	+	[[Category: Fukuhara H]]
-	[[Category: ~~Yumoto, K~~]]	+	[[Category: Fukushi S]]
-	[[Category: ~~Hashiguchi, T~~]]	+	[[Category: Hashiguchi T]]
-	[[Category: ~~Tonouchi,~~ K]]	+	[[Category: Higuchi Y]]
-	[[Category: ~~Anraku, Y~~]]	+	[[Category: Hoshino A]]
-	[[Category: ~~Adachi, Y~~]]	+	[[Category: Kita S]]
-	[[Category: ~~Suzuki, T~~]]	+	[[Category: Kotaki R]]
-	[[Category: Onodera, T]]	+	[[Category: Kuroda D]]
-	[[Category: ~~Kita, S~~]]	+	[[Category: Kuroda Y]]
-	[[Category: ~~Kuroda, D~~]]	+	[[Category: Maeda K]]
-	[[Category: ~~Maeda,~~ K]]	+	[[Category: Maenaka K]]
-	[[Category: ~~Muranishi, S~~]]	+	[[Category: Moriyama S]]
		+	[[Category: Muranishi S]]
		+	[[Category: Nakamura-Uchiyama F]]
		+	[[Category: Onodera T]]
		+	[[Category: Suzuki T]]
		+	[[Category: Takahashi Y]]
		+	[[Category: Tonouchi K]]
		+	[[Category: Yamamoto T]]
		+	[[Category: Yumoto K]]

OCA at 06:20, 28 December 2022

OCA — Wed, 28 Dec 2022 06:20:02 GMT

←Older revision		Revision as of 06:20, 28 December 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Moriyama, S., Anraku, Y., Muranishi, S., Adachi, Y., Kuroda, D., Higuchi, Y., Kotaki, R., Tonouchi, K., Yumoto, K., Suzuki, T., Kita, S., Fukuhara, H., Kuroda, Y., Yamamoto, T., Onodera, T., Fukushi, S., Maeda, K., Nakamura-Uchiyama, F., Hashiguchi, T., Hoshino, A., Maenaka, K., Takahashi, Y.		Authors: Moriyama, S., Anraku, Y., Muranishi, S., Adachi, Y., Kuroda, D., Higuchi, Y., Kotaki, R., Tonouchi, K., Yumoto, K., Suzuki, T., Kita, S., Fukuhara, H., Kuroda, Y., Yamamoto, T., Onodera, T., Fukushi, S., Maeda, K., Nakamura-Uchiyama, F., Hashiguchi, T., Hoshino, A., Maenaka, K., Takahashi, Y.

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

OCA — Thu, 24 Nov 2022 08:26:57 GMT

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

←Older revision

Revision as of 08:26, 24 November 2022

OCA: New page: '''Unreleased structure''' The entry 8hgm is ON HOLD Authors: Moriyama, S., Anraku, Y., Muranishi, S., Adachi, Y., Kuroda, D., Higuchi, Y., Kotaki, R., Tonouchi, K., Yumoto, K., Suzuki,...

OCA — Thu, 24 Nov 2022 08:26:56 GMT

New page: '''Unreleased structure''' The entry 8hgm is ON HOLD Authors: Moriyama, S., Anraku, Y., Muranishi, S., Adachi, Y., Kuroda, D., Higuchi, Y., Kotaki, R., Tonouchi, K., Yumoto, K., Suzuki,...

New page

'''Unreleased structure'''

The entry 8hgm is ON HOLD

Authors: Moriyama, S., Anraku, Y., Muranishi, S., Adachi, Y., Kuroda, D., Higuchi, Y., Kotaki, R., Tonouchi, K., Yumoto, K., Suzuki, T., Kita, S., Fukuhara, H., Kuroda, Y., Yamamoto, T., Onodera, T., Fukushi, S., Maeda, K., Nakamura-Uchiyama, F., Hashiguchi, T., Hoshino, A., Maenaka, K., Takahashi, Y.

Description: Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11
[[Category: Unreleased Structures]]
[[Category: Yamamoto, T]]
[[Category: Fukuhara, H]]
[[Category: Kuroda, Y]]
[[Category: Hoshino, A]]
[[Category: Kotaki, R]]
[[Category: Moriyama, S]]
[[Category: Higuchi, Y]]
[[Category: Fukushi, S]]
[[Category: Takahashi, Y]]
[[Category: Maenaka, K]]
[[Category: Nakamura-Uchiyama, F]]
[[Category: Yumoto, K]]
[[Category: Hashiguchi, T]]
[[Category: Tonouchi, K]]
[[Category: Anraku, Y]]
[[Category: Adachi, Y]]
[[Category: Suzuki, T]]
[[Category: Onodera, T]]
[[Category: Kita, S]]
[[Category: Kuroda, D]]
[[Category: Maeda, K]]
[[Category: Muranishi, S]]

8hgm - Revision history

OCA at 07:05, 25 October 2023

OCA at 06:20, 28 December 2022

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

OCA: New page: '''Unreleased structure''' The entry 8hgm is ON HOLD Authors: Moriyama, S., Anraku, Y., Muranishi, S., Adachi, Y., Kuroda, D., Higuchi, Y., Kotaki, R., Tonouchi, K., Yumoto, K., Suzuki,...