View source for 7yh7


==SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2)==
<StructureSection load='7yh7' size='340' side='right'caption='[[7yh7]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7yh7]] is a 9 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=7YH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YH7 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]] 3.3&#8491;</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=7yh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yh7 OCA], [https://pdbe.org/7yh7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yh7 RCSB], [https://www.ebi.ac.uk/pdbsum/7yh7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yh7 ProSAT]</span></td></tr>
</table>
<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.

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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7yh7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Severe acute respiratory syndrome coronavirus 2]]
[[Category: Adachi Y]]
[[Category: Anraku Y]]
[[Category: Fukuhara H]]
[[Category: Fukushi S]]
[[Category: Hashiguchi T]]
[[Category: Higuchi Y]]
[[Category: Hoshino A]]
[[Category: Kita S]]
[[Category: Kotaki R]]
[[Category: Kuroda D]]
[[Category: Kuroda Y]]
[[Category: Maeda K]]
[[Category: Maenaka K]]
[[Category: Moriyama S]]
[[Category: Muranishi S]]
[[Category: Nakamura-Uchiyama F]]
[[Category: Onodera T]]
[[Category: Someya T]]
[[Category: Suzuki T]]
[[Category: Takahashi Y]]
[[Category: Tonouchi K]]
[[Category: Yamamoto T]]
[[Category: Yumoto K]]