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	Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity.
Journal, issue, pages	Natl Sci Rev, Vol. 11, Issue 7, Page nwae206, Year 2024
Publish date	Jun 14, 2024
Authors	Pan Liu / Can Yue / Bo Meng / Tianhe Xiao / Sijie Yang / Shuo Liu / Fanchong Jian / Qianhui Zhu / Yuanling Yu / Yanyan Ren / Peng Wang / Yixin Li / Jinyue Wang / Xin Mao / Fei Shao / Youchun Wang / Ravindra Kumar Gupta / Yunlong Cao / Xiangxi Wang /
PubMed Abstract	Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional ...Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional glycosylation within the spike protein receptor-binding domain (RBD). Details of how the acquisition of glycosylation impacts viral fitness and human adaptation are not clearly understood. Here, we dissected the role of N354-linked glycosylation, acquired by BA.2.86 sub-lineages, as a RBD conformational control element in attenuating viral infectivity. The reduced infectivity is recovered in the presence of heparin sulfate, which targets the 'N354 pocket' to ease restrictions of conformational transition resulting in a 'RBD-up' state, thereby conferring an adjustable infectivity. Furthermore, N354 glycosylation improved spike cleavage and cell-cell fusion, and in particular escaped one subset of ADCC antibodies. Together with reduced immunogenicity in hybrid immunity background, these indicate a single spike amino acid glycosylation event provides selective advantage in humans through multiple mechanisms.
External links	Natl Sci Rev / PubMed:39071099 / PubMed Central
Methods	EM (single particle)
Resolution	3.18 - 7.97 Å
Structure data	37546 8whs EMDB-37546, PDB-8whs: Spike Trimer of BA.2.86 in complex with one hACE2 Method: EM (single particle) / Resolution: 3.33 Å 37548 8whu EMDB-37548, PDB-8whu: Spike Trimer of BA.2.86 in complex with two hACE2s Method: EM (single particle) / Resolution: 3.3 Å 37549 8whv EMDB-37549, PDB-8whv: Spike Trimer of BA.2.86 with three RBDs down Method: EM (single particle) / Resolution: 3.32 Å 37550 8whw EMDB-37550, PDB-8whw: Spike Trimer of BA.2.86 with single RBD up Method: EM (single particle) / Resolution: 3.85 Å 37553 8whz EMDB-37553, PDB-8whz: BA.2.86 RBD in complex with hACE2 (local refinement) Method: EM (single particle) / Resolution: 3.93 Å 38049 8x4h EMDB-38049, PDB-8x4h: SARS-CoV-2 JN.1 Spike Method: EM (single particle) / Resolution: 3.65 Å 38056 8x4z EMDB-38056, PDB-8x4z: BA.2.86 Spike Trimer with ins483V mutation (3 RBD down) Method: EM (single particle) / Resolution: 3.49 Å 38057 8x50 EMDB-38057, PDB-8x50: BA.2.86 Spike Trimer with ins483V mutation (1 RBD up) Method: EM (single particle) / Resolution: 3.82 Å 38063 8x55 EMDB-38063, PDB-8x55: BA.2.86 Spike Trimer with T356K mutation (3 RBD down) Method: EM (single particle) / Resolution: 3.75 Å 38064 8x56 EMDB-38064, PDB-8x56: BA.2.86 Spike Trimer with T356K mutation (1 RBD up) Method: EM (single particle) / Resolution: 3.93 Å 38072 8x5q EMDB-38072, PDB-8x5q: SARS-CoV-2 BA.2.75 Spike with K356T mutation (3 RBD down) Method: EM (single particle) / Resolution: 3.47 Å 38073 8x5r EMDB-38073, PDB-8x5r: SARS-CoV-2 BA.2.75 Spike with K356T mutation (1 RBD up) Method: EM (single particle) / Resolution: 3.72 Å 38681 8xur EMDB-38681, PDB-8xur: BA.2.86 Spike Trimer in complex with heparan sulfate Method: EM (single particle) / Resolution: 3.85 Å 38682 8xus EMDB-38682, PDB-8xus: JN.1 Spike Trimer in complex with heparan sulfate Method: EM (single particle) / Resolution: 3.18 Å 38683 8xut EMDB-38683, PDB-8xut: XBB.1.5 Spike Trimer in complex with heparan sulfate Method: EM (single particle) / Resolution: 3.2 Å 38684 8xuu EMDB-38684, PDB-8xuu: BA.2.86-T356K Spike Trimer in complex with heparan sulfate (Local refinement) Method: EM (single particle) / Resolution: 3.69 Å EMDB-38700: XBB.1.5-K356T S-trimer (1 RBD up) Method: EM (single particle) / Resolution: 7.97 Å EMDB-38701: XBB.1.5-K356T S-trimer (3 RBDs down) Method: EM (single particle) / Resolution: 4.37 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-ZN: Unknown entry ChemComp-CL: Unknown entry ChemComp-IDU: 2-O-sulfo-beta-L-altropyranuronic acid
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	VIRAL PROTEIN/HYDROLASE / surface protein / glycoprotein / spike protein / VIRAL PROTEIN-HYDROLASE complex / VIRAL PROTEIN / Timer / Trimer / Complex / Spike / SARS-CoV-2