8XLM

Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state)

Summary for 8XLM

• Entry DOI: 10.2210/pdb8xlm/pdb
• EMDB information: 38453
• 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: viral protein, 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: 496863.82

Authors

Nomai, T.,Anraku, Y.,Kita, S.,Hashiguchi, T.,Maenaka, K. (deposition date: 2023-12-26, release date: 2024-05-01, Last modification date: 2024-09-25)

Primary citation

Tsujino, S.,Deguchi, S.,Nomai, T.,Padilla-Blanco, M.,Plianchaisuk, A.,Wang, L.,Begum, M.M.,Uriu, K.,Mizuma, K.,Nao, N.,Kojima, I.,Tsubo, T.,Li, J.,Matsumura, Y.,Nagao, M.,Oda, Y.,Tsuda, M.,Anraku, Y.,Kita, S.,Yajima, H.,Sasaki-Tabata, K.,Guo, Z.,Hinay Jr., A.A.,Yoshimatsu, K.,Yamamoto, Y.,Nagamoto, T.,Asakura, H.,Nagashima, M.,Sadamasu, K.,Yoshimura, K.,Nasser, H.,Jonathan, M.,Putri, O.,Kim, Y.,Chen, L.,Suzuki, R.,Tamura, T.,Maenaka, K.,Irie, T.,Matsuno, K.,Tanaka, S.,Ito, J.,Ikeda, T.,Takayama, K.,Zahradnik, J.,Hashiguchi, T.,Fukuhara, T.,Sato, K.
Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.
Microbiol Immunol, 68:305-330, 2024

PubMed Abstract: In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.

PubMed: 38961765
DOI: 10.1111/1348-0421.13165

Experimental method

ELECTRON MICROSCOPY (3.22 Å)