ISDA

Deposition Date 2021-03-17

Release Date 2021-04-07

Last Version Date 2024-11-13

Entry Detail

PDB ID:

7NXC

Keywords:

VIRAL PROTEIN/HYDROLASE

Title:

Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with ACE2

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)
Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.14 Å

R-Value Free:

0.27

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Processed angiotensin-converting enzyme 2
Gene (Uniprot):ACE2
Chain IDs:A
Chain Length:604
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BYF1 Pfam ID:PF01401 EC:3.4.15.1

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:B
Chain Length:205
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Ligand Molecules

NAG

Primary Citation

Antibody evasion by the P.1 strain of SARS-CoV-2.

Dejnirattisai, W, Zhou, D, Supasa, P, Liu, C, Mentzer, A.J, Ginn, H.M, Zhao, Y, Duyvesteyn, H.M.E, Tuekprakhon, A, Nutalai, R, Wang, B, Lopez-Camacho, C, Slon-Campos, J, Walter, T.S, Skelly, D, Costa Clemens, S.A, Naveca, F.G, Nascimento, V, Nascimento, F, Fernandes da Costa, C, Resende, P.C, Pauvolid-Correa, A, Siqueira, M.M, Dold, C, Levin, R, Dong, T, Pollard, A.J, Knight, J.C, Crook, D, Lambe, T, Clutterbuck, E, Bibi, S, Flaxman, A, Bittaye, M, Belij-Rammerstorfer, S, Gilbert, S.C, Carroll, M.W, Klenerman, P, Barnes, E, Dunachie, S.J, Paterson, N.G, Williams, M.A, Hall, D.R, Hulswit, R.J.G, Bowden, T.A, Fry, E.E, Mongkolsapaya, J, Ren, J, Stuart, D.I, Screaton, G.R, Dejnirattisai, W, Zhou, D, Supasa, P, Liu, C, Mentzer, A.J, Ginn, H.M, Zhao, Y, Duyvesteyn, H.M, Tuekprakhon, A, Nutalai, R, Wang, B, Paesen, G.C, Lopez-Camacho, C, Slon-Campos, J, Walter, T.S, Skelly, D, Clemens, S.A.C, Naveca, F.G, Nascimento, V, Nascimento, F, Dold, C, Levin, R, Dong, T, Pollard, A.J, Knight, J.C, Crook, D, Lambe, T, Clutterbuck, E, Bibi, S, Flaxman, A, Bittaye, M, Belij-Rammerstorfer, S, Gilbert, S, Carroll, M.W, Klenerman, P, Barnes, E, Dunachie, S.J, Paterson, N.G, Williams, M.A, Hall, D.R, Hulswit, R.J.G, Bowden, T.A, Fry, E.E, Mongkolsapaya, J, Ren, J, Stuart, D.I, Screaton, G.R.Show

Cell 184 2939 ? (2021)

PMID: 33852911 DOI: 10.1016/j.cell.2021.03.055

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