View source for 8gz6


==Crystal structure of neutralizing VHH P17 in complex with SARS-CoV-2 Alpha variant spike receptor-binding domain==
<StructureSection load='8gz6' size='340' side='right'caption='[[8gz6]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8gz6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GZ6 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]] 1.35&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=8gz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gz6 OCA], [https://pdbe.org/8gz6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gz6 RCSB], [https://www.ebi.ac.uk/pdbsum/8gz6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gz6 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The continuous emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants associated with the adaptive evolution of the virus is prolonging the global coronavirus disease 2019 (COVID-19) pandemic. The modification of neutralizing antibodies based on structural information is expected to be a useful approach to rapidly combat emerging variants. A dimerized variable domain of heavy chain of heavy chain antibody (VHH) P17 that has highly potent neutralizing activity against SARS-CoV-2 has been reported but the mode of interaction with the epitope remains unclear. Here, we report the X-ray crystal structure of the complex of monomerized P17 bound to the SARS-CoV-2 receptor binding domain (RBD) and investigated the binding activity of P17 toward various variants of concern (VOCs) using kinetics measurements. The structure revealed details of the binding interface and showed that P17 had an appropriate linker length to have an avidity effect and recognize a wide range of RBD orientations. Furthermore, we identified mutations in known VOCs that decrease the binding affinity of P17 and proposed methods for the acquisition of affinity toward the Omicron RBD because Omicron is currently the most predominant VOC. This study provides information for the rational design of effective VHHs for emerging VOCs.

Structural insights into the rational design of a nanobody that binds with high affinity to the SARS-CoV-2 spike variant.,Yamaguchi K, Anzai I, Maeda R, Moriguchi M, Watanabe T, Imura A, Takaori-Kondo A, Inoue T J Biochem. 2023 Feb 3;173(2):115-127. doi: 10.1093/jb/mvac096. PMID:36413757<ref>PMID:36413757</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8gz6" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Vicugna pacos]]
[[Category: Anzai I]]
[[Category: Imura A]]
[[Category: Inoue T]]
[[Category: Maeda R]]
[[Category: Moriguchi M]]
[[Category: Takaori-Kondo A]]
[[Category: Watanabe T]]
[[Category: Yamaguchi K]]