7KIP

A 3.4 Angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles

This is a non-PDB format compatible entry.

Summary for 7KIP

• Entry DOI: 10.2210/pdb7kip/pdb
• EMDB information: 22889
• Descriptor: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (10 entities in total)
• Functional Keywords: nl63, in situ, spike trimer, glycosylation sites, single particle cryo-em, viral protein
• Biological source: Human coronavirus NL63 (HCoV-NL63)
• Total number of polymer chains: 3
• Total formula weight: 493459.55

Authors

Zhang, K.,Li, S.,Pintilie, G.,Chmielewski, D.,Schmid, M.,Simmons, G.,Jin, J.,Chiu, W. (deposition date: 2020-10-24, release date: 2020-11-11, Last modification date: 2024-10-23)

Primary citation

Zhang, K.,Li, S.,Pintilie, G.,Chmielewski, D.,Schmid, M.F.,Simmons, G.,Jin, J.,Chiu, W.
A 3.4- angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles.
Biorxiv, 2020

PubMed 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 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.

PubMed: 32817943
DOI: 10.1101/2020.08.11.245696

Experimental method

ELECTRON MICROSCOPY (3.39 Å)