Closed form exists in furin-cleaved and uncleaved S glycoprotein. The surface of its receptor-binding domain (RBD) is buried in the structure and not accessible to ACE2 receptor. Even though closed conformation has three-fold symmetry, cleaved is known to be more compact than the uncleaved closed structure

University of Michigan - Ann Arbor

Using cry-electron microscopy (cryo-EM), the structure of a furin protease-cleaved SARS-CoV-2 S glycoprotein was visualized. These particles were in three different types of conformations: closed, intermediate, and open with an upright receptor-binding domain (RBD). 

Structure of protease-cleaved SARS-CoV-2 S glycoprotein

Wrobel, A.G., Benton, D.J., Xu, P. et al. SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat Struct Mol Biol (2020). https://doi.org/10.1038/s41594-020-0468-7

SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects

Closed conformation of S glycoprotein

Intermediate form has 2 receptor-binding domains (RBD) that are buried, and a third RBD that is disordered. Two amino-terminal domains (NTD’s) have shifted their center of mass due to the close contact with the disordered RBD. 

Intermediate conformation of S glycoprotein

Open form is similar to intermediate form except the third RBD is exposed, allowing access for binding to ACE2 receptor. This conformation exists in uncleaved S glycoprotein. A lower number of S protein are found in a closed conformation for protease-cleaved.

Open conformation of S glycoprotein

"Three structures are calculated from micrographs of furin-cleaved material: closed, intermediate and open forms, of approximately equal proportions. In the uncleaved material, most of the population represents the closed form, and a small proportion is in the open conformation." 

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