7y6d

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'''Unreleased structure'''
 
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The entry 7y6d is ON HOLD
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==Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD==
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<StructureSection load='7y6d' size='340' side='right'caption='[[7y6d]], [[Resolution|resolution]] 4.39&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[7y6d]] is a 3 chain structure with sequence from [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=7Y6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Y6D FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.39&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7y6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7y6d OCA], [https://pdbe.org/7y6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7y6d RCSB], [https://www.ebi.ac.uk/pdbsum/7y6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7y6d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Among the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis of elevated pathogenicity using recombinant proteins, the architecture of intact Delta virions remains veiled. Moreover, pieces of molecular evidence for the detailed mechanism of S-mediated membrane fusion are missing. Here, we showed the pleomorphic nature of Delta virions from electron beam inactivated samples and reported the in situ structure and distribution of S on the authentic Delta variant. We also captured the virus-virus fusion events, which provided pieces of structural evidence for Delta's attenuated dependency on cellular factors for fusion activation, and proposed a model of S-mediated membrane fusion. Besides, site-specific glycan analysis revealed increased oligomannose-type glycosylation of native Delta S than that of the WT S. Together, these results disclose distinctive factors of Delta being the most virulent SARS-CoV-2 variant.
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Authors: Xu, J., Song, Y., Li, S.
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In situ architecture and membrane fusion of SARS-CoV-2 Delta variant.,Song Y, Yao H, Wu N, Xu J, Zhang Z, Peng C, Li S, Kong W, Chen Y, Zhu M, Wang J, Shi D, Zhao C, Lu X, Echavarria Galindo M, Li S Proc Natl Acad Sci U S A. 2023 May 2;120(18):e2213332120. doi: , 10.1073/pnas.2213332120. Epub 2023 Apr 24. PMID:37094167<ref>PMID:37094167</ref>
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Description: Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Li, S]]
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<div class="pdbe-citations 7y6d" style="background-color:#fffaf0;"></div>
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[[Category: Xu, J]]
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== References ==
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[[Category: Song, Y]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Severe acute respiratory syndrome coronavirus 2]]
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[[Category: Li S]]
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[[Category: Song Y]]
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[[Category: Xu J]]

Current revision

Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD

PDB ID 7y6d

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