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	Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Journal, issue, pages	EMBO J, Vol. 43, Issue 8, Page 1484-1498, Year 2024
Publish date	Mar 11, 2024
Authors	Weiwei Li / Zepeng Xu / Tianhui Niu / Yufeng Xie / Zhennan Zhao / Dedong Li / Qingwen He / Wenqiao Sun / Kaiyuan Shi / Wenjing Guo / Zhen Chang / Kefang Liu / Zheng Fan / Jianxun Qi / George F Gao /
PubMed Abstract	Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding ...Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the underlying mechanism of interplay between two factors remains incompletely understood. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. Based on the ACE2/RBD structures of these sub-variants and a comparison with the known complex structures, we found that R346T substitution in the RBD enhanced ACE2 binding upon an interaction with the residue R493, but not Q493, via a mechanism involving long-range conformation changes. Furthermore, we found that R493Q and F486V exert a balanced impact, through which immune evasion capability was somewhat compromised to achieve an optimal receptor binding. We propose a "two-steps-forward and one-step-backward" model to describe such a compromise between receptor binding affinity and immune evasion during RBD evolution of Omicron sub-variants.
External links	EMBO J / PubMed:38467833 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.47 - 3.47 Å
Structure data	37467 8wdy EMDB-37467, PDB-8wdy: SARS-CoV-2 Omicron BQ.1.1 RBD complexed with human ACE2 Method: EM (single particle) / Resolution: 2.69 Å 37468 8wdz EMDB-37468, PDB-8wdz: SARS-CoV-2 Omicron BQ.1 RBD complexed with human ACE2 Method: EM (single particle) / Resolution: 2.71 Å 37469 8we0 EMDB-37469, PDB-8we0: SARS-CoV-2 Omicron XBB RBD complexed with human ACE2 Method: EM (single particle) / Resolution: 2.8 Å 37470 8we1 EMDB-37470, PDB-8we1: SARS-CoV-2 Omicron BF.7 RBD complexed with human ACE2 Method: EM (single particle) / Resolution: 2.47 Å 37471 8we4 EMDB-37471, PDB-8we4: SARS-CoV-2 Omicron XBB.1.5 RBD complexed with human ACE2 and S304 Method: EM (single particle) / Resolution: 2.91 Å PDB-8wdr: Crystal structure of BQ.1.1 RBD complexed with human ACE2 Method: X-RAY DIFFRACTION / Resolution: 3.47 Å PDB-8wds: Crystal structure of BF.7 RBD complexed with human ACE2 Method: X-RAY DIFFRACTION / Resolution: 3.4 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	homo sapiens (human) severe acute respiratory syndrome coronavirus 2
Keywords	VIRAL PROTEIN / SARS-CoV-2 / BQ.1.1 / RBD / human ACE2 / BF.7 / VIRUS / VIRUS/IMMUNE SYSTEM / VIRUS-IMMUNE SYSTEM complex