National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
U24GM129564
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P41GM103832
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM079429
United States
Citation
Journal: bioRxiv / Year: 2020 Title: A 3.4-Å cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles. Authors: Kaiming Zhang / Shanshan Li / Grigore Pintilie / David Chmielewski / Michael F Schmid / Graham Simmons / Jing Jin / Wah Chiu Abstract: Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild ...Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV and SARS-CoV-2. Here we present the structure of HCoV-NL63 spike (S) trimer at 3.4-Å resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other amino acid positions as well as differences in glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. This structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.
History
Deposition
Oct 24, 2020
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Header (metadata) release
Nov 11, 2020
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Map release
Nov 11, 2020
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Update
Nov 11, 2020
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Current status
Nov 11, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
pH: 8 / Details: 20 mM Tris, pH 8.0, 120 mM NaCl, 1 mM EDTA
Grid
Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
Vitrification
Cryogen name: ETHANE
Details
HCoV-NL63 virions
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Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4138 / Average exposure time: 3.0 sec. / Average electron dose: 48.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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