7whk
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)== | ==The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)== | ||
| - | <StructureSection load='7whk' size='340' side='right'caption='[[7whk]]' scene=''> | + | <StructureSection load='7whk' size='340' side='right'caption='[[7whk]], [[Resolution|resolution]] 3.01Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WHK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7whk]] is a 8 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=7WHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WHK FirstGlance]. <br> |
| - | </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=7whk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7whk OCA], [https://pdbe.org/7whk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7whk RCSB], [https://www.ebi.ac.uk/pdbsum/7whk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7whk ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.01Å</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=7whk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7whk OCA], [https://pdbe.org/7whk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7whk RCSB], [https://www.ebi.ac.uk/pdbsum/7whk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7whk ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [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] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The effectiveness of SARS-CoV-2 vaccines and therapeutic antibodies have been limited by the continuous emergence of viral variants and by the restricted diffusion of antibodies from circulation into the sites of respiratory virus infection. Here, we report the identification of two highly conserved regions on the Omicron variant receptor-binding domain recognized by broadly neutralizing antibodies. Furthermore, we generated a bispecific single-domain antibody that was able to simultaneously and synergistically bind these two regions on a single Omicron variant receptor-binding domain as revealed by cryo-EM structures. We demonstrated that this bispecific antibody can be effectively delivered to lung via inhalation administration and exhibits exquisite neutralization breadth and therapeutic efficacy in mouse models of SARS-CoV-2 infections. Importantly, this study also deciphered an uncommon and highly conserved cryptic epitope within the spike trimeric interface that may have implications for the design of broadly protective SARS-CoV-2 vaccines and therapeutics. | ||
| + | |||
| + | Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody.,Li C, Zhan W, Yang Z, Tu C, Hu G, Zhang X, Song W, Du S, Zhu Y, Huang K, Kong Y, Zhang M, Mao Q, Gu X, Zhang Y, Xie Y, Deng Q, Song Y, Chen Z, Lu L, Jiang S, Wu Y, Sun L, Ying T Cell. 2022 Apr 14;185(8):1389-1401.e18. doi: 10.1016/j.cell.2022.03.009. Epub , 2022 Mar 10. PMID:35344711<ref>PMID:35344711</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7whk" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Antibody 3D structures|Antibody 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Homo sapiens]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Severe acute respiratory syndrome coronavirus 2]] | ||
[[Category: Chen ZG]] | [[Category: Chen ZG]] | ||
[[Category: Sun L]] | [[Category: Sun L]] | ||
[[Category: Zhan WQ]] | [[Category: Zhan WQ]] | ||
[[Category: Zhang X]] | [[Category: Zhang X]] | ||
Current revision
The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)
| |||||||||||
