6XE1 image
Deposition Date 2020-06-11
Release Date 2020-07-01
Last Version Date 2024-10-09
Entry Detail
PDB ID:
6XE1
Title:
Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a potent neutralizing antibody, CV30 Fab
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.75 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 63
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:C (auth: E)
Chain Length:273
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:CV30 Fab Heavy chain
Chain IDs:A (auth: H)
Chain Length:224
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:CV30 Fab Kappa chain
Chain IDs:B (auth: L)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation.
Nat Commun 11 5413 5413 (2020)
PMID: 33110068 DOI: 10.1038/s41467-020-19231-9

Abstact

SARS-CoV-2 is a betacoronavirus virus responsible for the COVID-19 pandemic. Here, we determine the X-ray crystal structure of a potent neutralizing monoclonal antibody, CV30, isolated from a patient infected with SARS-CoV-2, in complex with the receptor binding domain. The structure reveals that CV30 binds to an epitope that overlaps with the human ACE2 receptor binding motif providing a structural basis for its neutralization. CV30 also induces shedding of the S1 subunit, indicating an additional mechanism of neutralization. A germline reversion of CV30 results in a substantial reduction in both binding affinity and neutralization potential indicating the minimal somatic mutation is needed for potently neutralizing antibodies against SARS-CoV-2.

Legend

Protein

Chemical

Disease

Primary Citation of related structures