Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 8728, Year 2024
Publish date	Oct 9, 2024
Authors	Yuanchen Liu / Xiaoyu Zhao / Jialu Shi / Yajie Wang / Huan Liu / Ye-Fan Hu / Bingjie Hu / Huiping Shuai / Terrence Tsz-Tai Yuen / Yue Chai / Feifei Liu / Hua-Rui Gong / Jiayan Li / Xun Wang / Shujun Jiang / Xiang Zhang / Yanliang Zhang / Xiangnan Li / Lei Wang / Madeline Hartnoll / Tianrenzheng Zhu / Yuxin Hou / Xiner Huang / Chaemin Yoon / Yang Wang / Yixin He / Minmin Zhou / Lianzhao Du / Xiaojuan Zhang / Wan-Mui Chan / Lin-Lei Chen / Jian-Piao Cai / Shuofeng Yuan / Jie Zhou / Jian-Dong Huang / Kwok-Yung Yuen / Kelvin Kai-Wang To / Jasper Fuk-Woo Chan / Bao-Zhong Zhang / Lei Sun / Pengfei Wang / Hin Chu /
PubMed Abstract	SARS-CoV-2 JN.1 with an additional L455S mutation on spike when compared with its parental variant BA.2.86 has outcompeted all earlier variants to become the dominant circulating variant. Recent ...SARS-CoV-2 JN.1 with an additional L455S mutation on spike when compared with its parental variant BA.2.86 has outcompeted all earlier variants to become the dominant circulating variant. Recent studies investigated the immune resistance of SARS-CoV-2 JN.1 but additional factors are speculated to contribute to its global dominance, which remain elusive until today. Here, we find that SARS-CoV-2 JN.1 has a higher infectivity than BA.2.86 in differentiated primary human nasal epithelial cells (hNECs). Mechanistically, we demonstrate that the gained infectivity of SARS-CoV-2 JN.1 over BA.2.86 associates with increased entry efficiency conferred by L455S and better spike cleavage in hNECs. Structurally, S455 altered the mode of binding of JN.1 spike protein to ACE2 when compared to BA.2.86 spike at ACE2, and modified the internal structure of JN.1 spike protein by increasing the number of hydrogen bonds with neighboring residues. These findings indicate that a single mutation (L455S) enhances virus entry in hNECs and increases immune evasiveness, which contribute to the robust transmissibility of SARS-CoV-2 JN.1. We further evaluate the in vitro and in vivo virological characteristics between SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3, and identify key lineage-specific features of the two Omicron sublineages that contribute to our understanding on Omicron antigenicity, transmissibility, and pathogenicity.
External links	Nat Commun / PubMed:39379369 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 3.29 Å
Structure data	39688 8yzb EMDB-39688, PDB-8yzb: BA.2.86 RBD protein in complex with ACE2. Method: EM (single particle) / Resolution: 3.29 Å 39689 8yzc EMDB-39689, PDB-8yzc: Structure of BA.2.86 spike protein in complex with ACE2. Method: EM (single particle) / Resolution: 2.7 Å 39690 8yzd EMDB-39690, PDB-8yzd: Structure of JN.1 RBD protein in complex with ACE2. Method: EM (single particle) / Resolution: 3.07 Å 39691 8yze EMDB-39691, PDB-8yze: The JN.1 spike protein (S) in complex with ACE2. Method: EM (single particle) / Resolution: 3.06 Å
Source	homo sapiens (human) synthetic construct (others) severe acute respiratory syndrome coronavirus 2 enterobacteria phage t4 (virus) tequatrovirus t4
Keywords	VIRAL PROTEIN / ACE2