Coronavirus Cell Recognition

Tom Goddard
January 31, 2019

Look at coronavirus spike proteins and what molecules they recognized on host cells. An augmented reality video of this data is available.

We especially want to look at Wuhan coronavirus which is similar to SARS coronavirus and recognizes the same host cell angiotensin converting enzyme 2 (ACE2) protein. But we also look at a more benign human coronavirus (HCoV-OC43) that causes some cases of the common cold and instead recognizes sialic acid (as does influenza which is not a coronavirus). Coronaviruses cause 10-15% of cases of the common cold.

A ChimeraX session file is available along with all the data coronavirus.zip (1 Gbyte). The session file is coronavirus.cxs in the data subdirectory.

What do virus spikes look like?


Wuhan coronavirus	Influenza (EMDB 8088)	HIV virus (EMDB 3464) - fewer spikes

Common cold human coronavirus HCoV-OC43 recognizes sialic acid on human cells

Human coronavirus structure with sialic acid bound, 6nzk, June 2019, EMDB 0557 at 2.8 Angstrom resolution.


HCoV-OC43 spike electron microscopy.	Spike molecular model, glycosylation sites in orange.	Binding sialic acid (yellow).

SARS coronavirus recognizes ACE2 protein on human cells


SARS spike with green binding domain flipped up. Morph of 6acc to 6acd.	ACE2 (tan) bound to SARS spike. Morph of 6acg, 6acj, 6ack.

SARS spike 6acc, solved August 2018, 3.6 A EMDB 9588, one binding domain flipped up 6acd
yACE2 bound, 3 tilt angles 6acg, 6acj, 6ack.

Wuhan virus differences from SARS

Color SARS spike residues that are different in Wuhan virus.

GenBank sequence for Wuhan virus, MN908947.
More Wuhan sequences.
GenBank Wuhan glycoprotein sequence, QHD43416.

SARS neutralizing antibody S230

SARS neutralizing antibody S230 from a surviving patient 6nb7