View source for 7fbj


==Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6==
<StructureSection load='7fbj' size='340' side='right'caption='[[7fbj]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7fbj]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Chiloscyllium_plagiosum Chiloscyllium plagiosum] 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=7FBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FBJ 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]] 2.85&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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=7fbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fbj OCA], [https://pdbe.org/7fbj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fbj RCSB], [https://www.ebi.ac.uk/pdbsum/7fbj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fbj ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The identification of a novel class of shark-derived single domain antibodies, named vnarbodies that show picomolar affinities binding to the receptor binding domain (RBD) of Wuhan and Alpha, Beta, Kappa, Delta, Delta-plus, and Lambda variants, is reported. Vnarbody 20G6 and 17F6 have broad neutralizing activities against all these SARS-CoV-2 viruses as well as other sarbecoviruses, including Pangolin coronavirus and Bat coronavirus. Intranasal administration of 20G6 effectively protects mice from the challenges of SARS-CoV-2 Wuhan and Beta variants. 20G6 and 17F6 contain a unique "WXGY" motif in the complementary determining region 3 that binds to a hidden epitope on RBD, which is highly conserved in sarbecoviruses through a novel beta-sheet interaction. It is found that the S375F mutation on Omicron RBD disrupts the structure of beta-strand, thus impair the binding with 20G6. The study demonstrates that shark-derived vnarbodies offer a prophylactic and therapeutic option against most SARS-CoV-2 variants and provide insights into antibody evasion by the Omicron variant.

A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape.,Feng B, Chen Z, Sun J, Xu T, Wang Q, Yi H, Niu X, Zhu J, Fan M, Hou R, Shao Y, Huang S, Li C, Hu P, Zheng P, He P, Luo J, Yan Q, Xiong X, Liu J, Zhao J, Chen L Small Methods. 2022 Jul;6(7):e2200387. doi: 10.1002/smtd.202200387. Epub 2022 May , 18. PMID:35583124<ref>PMID:35583124</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7fbj" style="background-color:#fffaf0;"></div>

==See Also==
*[[Spike protein 3D structures|Spike protein 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Chiloscyllium plagiosum]]
[[Category: Large Structures]]
[[Category: Severe acute respiratory syndrome coronavirus 2]]
[[Category: Feng B]]
[[Category: Liu J]]
[[Category: Xu T]]
[[Category: Zhu J]]