7DEU image
Deposition Date 2020-11-05
Release Date 2021-03-31
Last Version Date 2024-11-13
Entry Detail
PDB ID:
7DEU
Title:
Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 43 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:A
Chain Length:206
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:antibody scFv
Chain IDs:B
Chain Length:253
Number of Molecules:1
Biological Source:Mus musculus
Ligand Molecules
Primary Citation
Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.
Plos Biol. 19 e3001209 e3001209 (2021)
PMID: 33961621 DOI: 10.1371/journal.pbio.3001209

Abstact

The ongoing Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) threatens global public health and economy unprecedentedly, requiring accelerating development of prophylactic and therapeutic interventions. Molecular understanding of neutralizing antibodies (NAbs) would greatly help advance the development of monoclonal antibody (mAb) therapy, as well as the design of next generation recombinant vaccines. Here, we applied H2L2 transgenic mice encoding the human immunoglobulin variable regions, together with a state-of-the-art antibody discovery platform to immunize and isolate NAbs. From a large panel of isolated antibodies, 25 antibodies showed potent neutralizing activities at sub-nanomolar levels by engaging the spike receptor-binding domain (RBD). Importantly, one human NAb, termed PR1077, from the H2L2 platform and 2 humanized NAb, including PR953 and PR961, were further characterized and subjected for subsequent structural analysis. High-resolution X-ray crystallography structures unveiled novel epitopes on the receptor-binding motif (RBM) for PR1077 and PR953, which directly compete with human angiotensin-converting enzyme 2 (hACE2) for binding, and a novel non-blocking epitope on the neighboring site near RBM for PR961. Moreover, we further tested the antiviral efficiency of PR1077 in the Ad5-hACE2 transduction mouse model of COVID-19. A single injection provided potent protection against SARS-CoV-2 infection in either prophylactic or treatment groups. Taken together, these results shed light on the development of mAb-related therapeutic interventions for COVID-19.

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