8r1d: Difference between revisions
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==SD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein== | |||
<StructureSection load='8r1d' size='340' side='right'caption='[[8r1d]], [[Resolution|resolution]] 2.37Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8r1d]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8R1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8R1D 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]] 2.37Å</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=8r1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8r1d OCA], [https://pdbe.org/8r1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8r1d RCSB], [https://www.ebi.ac.uk/pdbsum/8r1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8r1d ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response. | |||
The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86.,Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR Nat Commun. 2024 Mar 28;15(1):2734. doi: 10.1038/s41467-024-46982-6. PMID:38548763<ref>PMID:38548763</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8r1d" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia virus T4]] | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Duyvesteyn HME]] | |||
[[Category: Ren J]] | |||
[[Category: Stuart DI]] | |||
Latest revision as of 12:52, 17 October 2024
SD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike GlycoproteinSD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
Structural highlights
Publication Abstract from PubMedUnder pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response. The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86.,Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR Nat Commun. 2024 Mar 28;15(1):2734. doi: 10.1038/s41467-024-46982-6. PMID:38548763[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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