7RKU image
Deposition Date 2021-07-22
Release Date 2021-09-22
Last Version Date 2024-11-13
Entry Detail
PDB ID:
7RKU
Title:
Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 61
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:A, B, C, D
Chain Length:212
Number of Molecules:4
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:C022 Antibody Fab Heavy Chain
Chain IDs:E, G, H, J
Chain Length:240
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:C022 Antibody Fab Light Chain
Chain IDs:F, I, K, L
Chain Length:215
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.
Cell Rep 36 109760 109760 (2021)
PMID: 34534459 DOI: 10.1016/j.celrep.2021.109760

Abstact

Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding domains (RBDs). Potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly emergent zoonotic sarbecoviruses and variants, but they usually show only weak neutralization potencies. Here, we characterize two class 4 anti-RBD antibodies derived from coronavirus disease 2019 (COVID-19) donors that exhibit breadth and potent neutralization of zoonotic coronaviruses and SARS-CoV-2 variants. C118-RBD and C022-RBD structures reveal orientations that extend from the cryptic epitope to occlude ACE2 binding and CDRH3-RBD main-chain H-bond interactions that extend an RBD β sheet, thus reducing sensitivity to RBD side-chain changes. A C118-spike trimer structure reveals rotated RBDs that allow access to the cryptic epitope and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
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