8dm4: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-'''Unreleased structure'''
-The entry 8dm4 is ON HOLD
+==Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)==
+<StructureSection load='8dm4' size='340' side='right'caption='[[8dm4]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8dm4]] is a 3 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=8DM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DM4 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]] 2.45&#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=8dm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dm4 OCA], [https://pdbe.org/8dm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dm4 RCSB], [https://www.ebi.ac.uk/pdbsum/8dm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dm4 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The BA.2 sub-lineage of the Omicron (B.1.1.529) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant rapidly supplanted the original BA.1 sub-lineage in early 2022. Both lineages threatened the efficacy of vaccine-elicited antibodies and acquired increased binding to several mammalian ACE2 receptors. Cryoelectron microscopy (cryo-EM) analysis of the BA.2 spike (S) glycoprotein in complex with mouse ACE2 (mACE2) identifies BA.1- and BA.2-mutated residues Q493R, N501Y, and Y505H as complementing non-conserved residues between human and mouse ACE2, rationalizing the enhanced S protein-mACE2 interaction for Omicron variants. Cryo-EM structures of the BA.2 S-human ACE2 complex and of the extensively mutated BA.2 amino-terminal domain (NTD) reveal a dramatic reorganization of the highly antigenic N1 loop into a beta-strand, providing an explanation for decreased binding of the BA.2 S protein to antibodies isolated from BA.1-convalescent patients. Our analysis reveals structural mechanisms underlying the antigenic drift in the rapidly evolving Omicron variant landscape.
-Authors: Zhu, X., Saville, J.W., Mannar, D., Berezuk, A.M., Cholak, S., Tuttle, K.S., Vahdatihassani, F., Subramaniam, S.
+Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.,Saville JW, Mannar D, Zhu X, Berezuk AM, Cholak S, Tuttle KS, Vahdatihassani F, Subramaniam S Cell Rep. 2023 Jan 31;42(1):111964. doi: 10.1016/j.celrep.2022.111964. Epub 2023 , Jan 4. PMID:36640338<ref>PMID:36640338</ref>
-Description: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Subramaniam, S]]
+<div class="pdbe-citations 8dm4" style="background-color:#fffaf0;"></div>
-[[Category: Zhu, X]]
-[[Category: Tuttle, K.S]]
+==See Also==
-[[Category: Mannar, D]]
+*[[Spike protein 3D structures|Spike protein 3D structures]]
-[[Category: Saville, J.W]]
+== References ==
-[[Category: Vahdatihassani, F]]
+<references/>
-[[Category: Cholak, S]]
+__TOC__
-[[Category: Berezuk, A.M]]
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Severe acute respiratory syndrome coronavirus 2]]
+[[Category: Berezuk AM]]
+[[Category: Cholak S]]
+[[Category: Mannar D]]
+[[Category: Saville JW]]
+[[Category: Subramaniam S]]
+[[Category: Tuttle KS]]
+[[Category: Vahdatihassani F]]
+[[Category: Zhu X]]