View source for 7tf1


==Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein (focused refinement of RBD)==
<StructureSection load='7tf1' size='340' side='right'caption='[[7tf1]], [[Resolution|resolution]] 3.57&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TF1 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]] 3.57&#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=7tf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tf1 OCA], [https://pdbe.org/7tf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7tf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tf1 ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
The Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a structural head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation and with unknown biological implications. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant.

Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants.,Saville JW, Mannar D, Zhu X, Srivastava SS, Berezuk AM, Demers JP, Zhou S, Tuttle KS, Sekirov I, Kim A, Li W, Dimitrov DS, Subramaniam S Nat Commun. 2022 Feb 8;13(1):742. doi: 10.1038/s41467-022-28324-6. PMID:35136050<ref>PMID:35136050</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 7tf1" style="background-color:#fffaf0;"></div>

==See Also==
*[[Antibody 3D structures|Antibody 3D structures]]
*[[Spike protein 3D structures|Spike protein 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Berezuk AM]]
[[Category: Demers JP]]
[[Category: Mannar D]]
[[Category: Saville JW]]
[[Category: Srivastava SS]]
[[Category: Subramaniam S]]
[[Category: Tuttle KS]]
[[Category: Zhou S]]
[[Category: Zhu X]]