ISDA

Entry Detail

PDB ID:

7CH5

Keywords:

PROTEIN BINDING/IMMUNE SYSTEM

Title:

Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab

Biological Source:

Source Organism:

Homo sapiens, Severe acute respiratory syndrome coronavirus 2

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2020-07-05

Release Date:

2020-09-16

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 21 21 21

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Macromolecular Entities

Polymer Type:polypeptide(L)
Description:BD-629 Fab H
Chain IDs:A (auth: H)
Chain Length:222
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Description:BD-629 Fab L
Chain IDs:B (auth: L)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:C (auth: R)
Chain Length:223
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Ligand Molecules

Primary Citation

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.

Du, S, Cao, Y, Zhu, Q, Yu, P, Qi, F, Wang, G, Du, X, Bao, L, Deng, W, Zhu, H, Liu, J, Nie, J, Zheng, Y, Liang, H, Liu, R, Gong, S, Xu, H, Yisimayi, A, Lv, Q, Wang, B, He, R, Han, Y, Zhao, W, Bai, Y, Qu, Y, Gao, X, Ji, C, Wang, Q, Gao, N, Huang, W, Wang, Y, Xie, X.S, Su, X.D, Xiao, J, Qin, C.Show

Cell 183 1013 1023.e13 (2020)

PMID: 32970990 DOI: 10.1016/j.cell.2020.09.035

Abstact

Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; however, its neutralization mechanism is largely unknown. Here, we report the 3.5-Å cryo-EM structure of BD-368-2/trimeric-spike complex, revealing that BD-368-2 fully blocks ACE2 recognition by occupying all three receptor-binding domains (RBDs) simultaneously, regardless of their "up" or "down" conformations. Also, BD-368-2 treats infected adult hamsters at low dosages and at various administering windows, in contrast to placebo hamsters that manifested severe interstitial pneumonia. Moreover, BD-368-2's epitope completely avoids the common binding site of VH3-53/VH3-66 recurrent NAbs, evidenced by tripartite co-crystal structures with RBDs. Pairing BD-368-2 with a potent recurrent NAb neutralizes SARS-CoV-2 pseudovirus at pM level and rescues mutation-induced neutralization escapes. Together, our results rationalized a new RBD epitope that leads to high neutralization potency and demonstrated BD-368-2's therapeutic potential in treating COVID-19.

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