Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function

The B.1.1.7 variant of SARS-CoV-2 first detected in the UK harbors amino-acid substitutions and deletions in the spike protein that potentially enhance host angiotensin conversion enzyme 2 (ACE2) receptor binding and viral immune evasion. Here we report cryo-EM structures of the spike protein of B.1.1.7 in the apo and ACE2-bound forms. The apo form showed one or two receptor-binding domains (RBDs) in the open conformation, without populating the fully closed state. All three RBDs were engaged in ACE2 binding. The B.1.1.7-specific A570D mutation introduces a molecular switch that could modulate the opening and closing of the RBD. The N501Y mutation introduces a pi-pi interaction that enhances RBD binding to ACE2 and abolishes binding of a potent neutralizing antibody (nAb). Cryo-EM also revealed how a cocktail of two nAbs simultaneously bind to all three RBDs, and demonstrated the potency of the nAb cocktail to neutralize different SARS-CoV-2 pseudovirus strains, including B.1.1.7. Cryo-EM structures and functional analyses of the SARS-CoV-2 B.1.1.7 variant spike protein reveal that the A570D mutation creates a molecular switch to regulate up-down conformations of the ACE2 receptor-binding domain through a pedal-bin-like mechanism.

Automated summary

The spike protein of the SARS-CoV-2 B.1.1.7 variant exhibits mutations that affect virus binding to the host ACE2 receptor and immune evasion. The A570D and N501Y mutations have been shown to impact the stability of the spike protein structure, and an introduced neutralizing antibody can effectively neutralize different strains of the virus.