ISDA

Entry Detail

PDB ID:

7U2E

Keywords:

VIRAL PROTEIN/IMMUNE SYSTEM

Title:

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2, Homo sapiens

Host Organism:

Trichoplusia ni

PDB Version:

Deposition Date:

2022-02-23

Release Date:

2022-05-04

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.85 Å

R-Value Free:

0.28

R-Value Work:

0.25

R-Value Observed:

0.25

Space Group:

P 41

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:A
Chain Length:205
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Polymer Type:polypeptide(L)
Description:ADI-55688 heavy chain
Chain IDs:B (auth: H)
Chain Length:227
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Description:ADI-55688 light chain
Chain IDs:C (auth: L)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

NAG

SO4

Primary Citation

A broad and potent neutralization epitope in SARS-related coronaviruses.

Yuan, M, Zhu, X, He, W.T, Zhou, P, Kaku, C.I, Capozzola, T, Zhu, C.Y, Yu, X, Liu, H, Yu, W, Hua, Y, Tien, H, Peng, L, Song, G, Cottrell, C.A, Schief, W.R, Nemazee, D, Walker, L.M, Andrabi, R, Burton, D.R, Wilson, I.A, Yuan, M, Zhu, X, He, W.T, Zhou, P, Kaku, C.I, Capozzola, T, Zhu, C.Y, Yu, X, Liu, H, Yu, W, Hua, Y, Tien, H, Peng, L, Song, G, Cottrell, C.A, Schief, W.R, Nemazee, D, Walker, L.M, Andrabi, R, Burton, D.R, Wilson, I.A.Show

Proc.Natl.Acad.Sci.USA 119 e2205784119 e2205784119 (2022)

PMID: 35767670 DOI: 10.1073/pnas.2205784119

Abstact

Many neutralizing antibodies (nAbs) elicited to ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through natural infection and vaccination have reduced effectiveness to SARS-CoV-2 variants. Here, we show that therapeutic antibody ADG20 is able to neutralize SARS-CoV-2 variants of concern (VOCs) including Omicron (B.1.1.529) as well as other SARS-related coronaviruses. We delineate the structural basis of this relatively escape-resistant epitope that extends from one end of the receptor binding site (RBS) into the highly conserved CR3022 site. ADG20 can then benefit from high potency through direct competition with ACE2 in the more variable RBS and interaction with the more highly conserved CR3022 site. Importantly, antibodies that are able to target this site generally neutralize a broad range of VOCs, albeit with reduced potency against Omicron. Thus, this conserved and vulnerable site can be exploited for the design of universal vaccines and therapeutic antibodies.

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