7E5Y | pdb_00007e5y

Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD

PDB DOI: https://doi.org/10.2210/pdb7E5Y/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-02-21 Released: 2021-06-23
Deposition Author(s): Wu, H., Yu, F., Wang, Q.S., Zhou, H., Wang, W.W., Zhao, T., Pan, Y.B., Yang, X.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.59 Å
R-Value Free:
0.277 (Depositor), 0.281 (DCC)
R-Value Work:
0.232 (Depositor), 0.233 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Screening of potent neutralizing antibodies against SARS-CoV-2 using convalescent patients-derived phage-display libraries.

Pan, Y., Du, J., Liu, J., Wu, H., Gui, F., Zhang, N., Deng, X., Song, G., Li, Y., Lu, J., Wu, X., Zhan, S., Jing, Z., Wang, J., Yang, Y., Liu, J., Chen, Y., Chen, Q., Zhang, H., Hu, H., Duan, K., Wang, M., Wang, Q., Yang, X.

(2021) Cell Discov 7: 57-57

PubMed: 34315862 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-021-00295-w
Primary Citation Related Structures:
7E5Y

PubMed Abstract:
As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to threaten public health worldwide, the development of effective interventions is urgently needed. Neutralizing antibodies (nAbs) have great potential for the prevention and treatment of SARS-CoV-2 infection. In this study, ten nAbs were isolated from two phage-display immune libraries constructed from the pooled PBMCs of eight COVID-19 convalescent patients. Eight of them, consisting of heavy chains encoded by the immunoglobulin heavy-chain gene-variable region (IGHV)3-66 or IGHV3-53 genes, recognized the same epitope on the receptor-binding domain (RBD), while the remaining two bound to different epitopes. Among the ten antibodies, 2B11 exhibited the highest affinity and neutralization potency against the original wild-type (WT) SARS-CoV-2 virus (K _D = 4.76 nM for the S1 protein, IC ₅₀ = 6 ng/mL for pseudoviruses, and IC ₅₀ = 1 ng/mL for authentic viruses), and potent neutralizing ability against B.1.1.7 pseudoviruses. Furthermore, 1E10, targeting a distinct epitope on RBD, exhibited different neutralization efficiency against WT SARS-CoV-2 and its variants B.1.1.7, B.1.351, and P.1. The crystal structure of the 2B11-RBD complexes revealed that the epitope of 2B11 highly overlaps with the ACE2-binding site. The in vivo experiment of 2B11 using AdV5-hACE2-transduced mice showed encouraging therapeutic and prophylactic efficacy against SARS-CoV-2. Taken together, our results suggest that the highly potent SARS-CoV-2-neutralizing antibody, 2B11, could be used against the WT SARS-CoV-2 and B.1.1.7 variant, or in combination with a different epitope-targeted neutralizing antibody, such as 1E10, against SARS-CoV-2 variants.

Organizational Affiliation

National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China.

Macromolecule Content

Total Structure Weight: 144.04 kDa
Atom Count: 9,297
Modeled Residue Count: 1,215
Deposited Residue Count: 1,324
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth R], D [auth A]	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence