7NXA image
Entry Detail
PDB ID:
7NXA
Title:
Crystal structure of the receptor binding domain of SARS-CoV-2 B.1.351 variant Spike glycoprotein in complex with COVOX-222 and EY6A Fabs
Biological Source:
PDB Version:
Deposition Date:
2021-03-17
Release Date:
2021-04-07
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:COVOX-222 Fab heavy chain
Chain IDs:D (auth: A)
Chain Length:224
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:COVOX-222 Fab light chain
Chain IDs:E (auth: B)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:C (auth: E)
Chain Length:205
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Description:EY6A Fab heavy chain
Chain IDs:A (auth: H)
Chain Length:226
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:EY6A Fab light chain
Chain IDs:B (auth: L)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation

Abstact

Terminating the SARS-CoV-2 pandemic relies upon pan-global vaccination. Current vaccines elicit neutralizing antibody responses to the virus spike derived from early isolates. However, new strains have emerged with multiple mutations, including P.1 from Brazil, B.1.351 from South Africa, and B.1.1.7 from the UK (12, 10, and 9 changes in the spike, respectively). All have mutations in the ACE2 binding site, with P.1 and B.1.351 having a virtually identical triplet (E484K, K417N/T, and N501Y), which we show confer similar increased affinity for ACE2. We show that, surprisingly, P.1 is significantly less resistant to naturally acquired or vaccine-induced antibody responses than B.1.351, suggesting that changes outside the receptor-binding domain (RBD) impact neutralization. Monoclonal antibody (mAb) 222 neutralizes all three variants despite interacting with two of the ACE2-binding site mutations. We explain this through structural analysis and use the 222 light chain to largely restore neutralization potency to a major class of public antibodies.

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Primary Citation of related structures