8XUX
Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)
Summary for 8XUX
| Entry DOI | 10.2210/pdb8xux/pdb |
| EMDB information | 38459 |
| Descriptor | Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total) |
| Functional Keywords | spike protein, glycoprotein, virus, viral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV,SARS-CoV-2) |
| Total number of polymer chains | 3 |
| Total formula weight | 422707.12 |
| Authors | Yajima, H.,Anraku, Y.,Kita, S.,Kimura, K.,Maenaka, K.,Hashiguchi, T. (deposition date: 2024-01-14, release date: 2024-10-09, Last modification date: 2024-10-23) |
| Primary citation | Yajima, H.,Anraku, Y.,Kaku, Y.,Kimura, K.T.,Plianchaisuk, A.,Okumura, K.,Nakada-Nakura, Y.,Atarashi, Y.,Hemmi, T.,Kuroda, D.,Takahashi, Y.,Kita, S.,Sasaki, J.,Sumita, H.,Ito, J.,Maenaka, K.,Sato, K.,Hashiguchi, T. Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1. Nat Commun, 15:8574-8574, 2024 Cited by PubMed Abstract: Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the RBD in the down-conformation to facilitate the conformational shift to RBD-up remains unclear. Herein, we present the structures of the BA.2.86 and the JN.1 spike proteins bound to ACE2. Notably, we successfully observed the ACE2-bound down-RBD, indicating an intermediate structure before the RBD-up conformation. The wider and mobile angle of RBDs in the up-state provides space for ACE2 to interact with the down-RBD, facilitating the transition to the RBD-up state. The K356T, but not N354-linked glycan, contributes to both of infectivity and neutralizing-antibody evasion in BA.2.86. These structural insights the spike-protein dynamics would help understand the mechanisms underlying SARS-CoV-2 infection and its neutralization. PubMed: 39375326DOI: 10.1038/s41467-024-52808-2 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.22 Å) |
Structure validation
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