7MF1 image
Deposition Date 2021-04-08
Release Date 2021-05-12
Last Version Date 2024-11-06
Entry Detail
PDB ID:
7MF1
Title:
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 47D1
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.09 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
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:205
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:47D1 Fab heavy chain
Chain IDs:B (auth: H)
Chain Length:230
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:47D1 Fab light chain
Chain IDs:C (auth: L)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Diverse immunoglobulin gene usage and convergent epitope targeting in neutralizing antibody responses to SARS-CoV-2.
Cell Rep 35 109109 109109 (2021)
PMID: 33932326 DOI: 10.1016/j.celrep.2021.109109

Abstact

It is unclear whether individuals with enormous diversity in B cell receptor repertoires are consistently able to mount effective antibody responses against SARS-CoV-2. We analyzed antibody responses in a cohort of 55 convalescent patients and isolated 54 potent neutralizing monoclonal antibodies (mAbs). While most of the mAbs target the angiotensin-converting enzyme 2 (ACE2) binding surface on the receptor binding domain (RBD) of SARS-CoV-2 spike protein, mAb 47D1 binds only to one side of the receptor binding surface on the RBD. Neutralization by 47D1 is achieved independent of interfering RBD-ACE2 binding. A crystal structure of the mAb-RBD complex shows that the IF motif at the tip of 47D1 CDR H2 interacts with a hydrophobic pocket in the RBD. Diverse immunoglobulin gene usage and convergent epitope targeting characterize neutralizing antibody responses to SARS-CoV-2, suggesting that vaccines that effectively present the receptor binding site on the RBD will likely elicit neutralizing antibody responses in a large fraction of the population.

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Primary Citation of related structures