8JYN
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)
Summary for 8JYN
| Entry DOI | 10.2210/pdb8jyn/pdb |
| EMDB information | 36727 |
| Descriptor | Spike glycoprotein, Processed angiotensin-converting enzyme 2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total) |
| Functional Keywords | spike protein, glycoprotein, virus, viral protein-protein binding complex, viral protein/protein binding |
| Biological source | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2) More |
| Total number of polymer chains | 4 |
| Total formula weight | 497378.24 |
| Authors | Yajima, H.,Anraku, Y.,Kita, S.,Kimura, K.,Sasaki, J.,Sasaki-Tabata, K.,Maenaka, K.,Hashiguchi, T. (deposition date: 2023-07-03, release date: 2024-01-03, Last modification date: 2025-01-15) |
| Primary citation | Tamura, T.,Irie, T.,Deguchi, S.,Yajima, H.,Tsuda, M.,Nasser, H.,Mizuma, K.,Plianchaisuk, A.,Suzuki, S.,Uriu, K.,Begum, M.M.,Shimizu, R.,Jonathan, M.,Suzuki, R.,Kondo, T.,Ito, H.,Kamiyama, A.,Yoshimatsu, K.,Shofa, M.,Hashimoto, R.,Anraku, Y.,Kimura, K.T.,Kita, S.,Sasaki, J.,Sasaki-Tabata, K.,Maenaka, K.,Nao, N.,Wang, L.,Oda, Y.,Ikeda, T.,Saito, A.,Matsuno, K.,Ito, J.,Tanaka, S.,Sato, K.,Hashiguchi, T.,Takayama, K.,Fukuhara, T. Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant. Nat Commun, 15:1176-1176, 2024 Cited by PubMed Abstract: Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5. PubMed: 38332154DOI: 10.1038/s41467-024-45274-3 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.04 Å) |
Structure validation
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