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Structure paper

TitleSpike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity.
Journal, issue, pagesNatl Sci Rev, Vol. 11, Issue 7, Page nwae206, Year 2024
Publish dateJun 14, 2024
AuthorsPan 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 AbstractSelective 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 linksNatl Sci Rev / PubMed:39071099 / PubMed Central
MethodsEM (single particle)
Resolution3.18 - 7.97 Å
Structure data

EMDB-37546, PDB-8whs:
Spike Trimer of BA.2.86 in complex with one hACE2
Method: EM (single particle) / Resolution: 3.33 Å

EMDB-37548, PDB-8whu:
Spike Trimer of BA.2.86 in complex with two hACE2s
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-37549, PDB-8whv:
Spike Trimer of BA.2.86 with three RBDs down
Method: EM (single particle) / Resolution: 3.32 Å

EMDB-37550, PDB-8whw:
Spike Trimer of BA.2.86 with single RBD up
Method: EM (single particle) / Resolution: 3.85 Å

EMDB-37553, PDB-8whz:
BA.2.86 RBD in complex with hACE2 (local refinement)
Method: EM (single particle) / Resolution: 3.93 Å

EMDB-38049, PDB-8x4h:
SARS-CoV-2 JN.1 Spike
Method: EM (single particle) / Resolution: 3.65 Å

EMDB-38056, PDB-8x4z:
BA.2.86 Spike Trimer with ins483V mutation (3 RBD down)
Method: EM (single particle) / Resolution: 3.49 Å

EMDB-38057, PDB-8x50:
BA.2.86 Spike Trimer with ins483V mutation (1 RBD up)
Method: EM (single particle) / Resolution: 3.82 Å

EMDB-38063, PDB-8x55:
BA.2.86 Spike Trimer with T356K mutation (3 RBD down)
Method: EM (single particle) / Resolution: 3.75 Å

EMDB-38064, PDB-8x56:
BA.2.86 Spike Trimer with T356K mutation (1 RBD up)
Method: EM (single particle) / Resolution: 3.93 Å

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

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

EMDB-38681, PDB-8xur:
BA.2.86 Spike Trimer in complex with heparan sulfate
Method: EM (single particle) / Resolution: 3.85 Å

EMDB-38682, PDB-8xus:
JN.1 Spike Trimer in complex with heparan sulfate
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-38683, PDB-8xut:
XBB.1.5 Spike Trimer in complex with heparan sulfate
Method: EM (single particle) / Resolution: 3.2 Å

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)
KeywordsVIRAL PROTEIN/HYDROLASE / surface protein / glycoprotein / spike protein / VIRAL PROTEIN-HYDROLASE complex / VIRAL PROTEIN / Timer / Trimer / Complex / Spike / SARS-CoV-2

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