8HRD image
Entry Detail
PDB ID:
8HRD
Title:
Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab
Biological Source:
PDB Version:
Deposition Date:
2022-12-15
Release Date:
2023-12-20
Method Details:
Experimental Method:
Resolution:
2.86 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:A, F (auth: B), K, P (auth: T)
Chain Length:223
Number of Molecules:4
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Description:W14 Fab heavy chain
Chain IDs:D, I (auth: G), N, S (auth: Y)
Chain Length:234
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:W14 Fab light chain
Chain IDs:E (auth: F), J (auth: H), O (auth: Q), T (auth: Z)
Chain Length:215
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:IMCAS74 Fab heavy chain
Chain IDs:B (auth: O), G (auth: C), L, Q (auth: W)
Chain Length:235
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:IMCAS74 Fab light chain
Chain IDs:C (auth: P), H (auth: E), M, R (auth: X)
Chain Length:217
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Proc.Natl.Acad.Sci.USA 120 e2314193120 e2314193120 (2023)
PMID: 38109549 DOI: 10.1073/pnas.2314193120

Abstact

Currently, monoclonal antibodies (MAbs) targeting the SARS-CoV-2 receptor binding domain (RBD) of spike (S) protein are classified into seven classes based on their binding epitopes. However, most of these antibodies are seriously impaired by SARS-CoV-2 Omicron and its subvariants, especially the recent BQ.1.1, XBB and its derivatives. Identification of broadly neutralizing MAbs against currently circulating variants is imperative. In this study, we identified a "breathing" cryptic epitope in the S protein, named as RBD-8. Two human MAbs, BIOLS56 and IMCAS74, were isolated recognizing this epitope with broad neutralization abilities against tested sarbecoviruses, including SARS-CoV, pangolin-origin coronaviruses, and all the SARS-CoV-2 variants tested (Omicron BA.4/BA.5, BQ.1.1, and XBB subvariants). Searching through the literature, some more RBD-8 MAbs were defined. More importantly, BIOLS56 rescues the immune-evaded antibody, RBD-5 MAb IMCAS-L4.65, by making a bispecific MAb, to neutralize BQ.1 and BQ.1.1, thereby producing an MAb to cover all the currently circulating Omicron subvariants. Structural analysis reveals that the neutralization effect of RBD-8 antibodies depends on the extent of epitope exposure, which is affected by the angle of antibody binding and the number of up-RBDs induced by angiotensin-converting enzyme 2 binding. This cryptic epitope which recognizes non- receptor binding motif (non-RBM) provides guidance for the development of universal therapeutic antibodies and vaccines against COVID-19.

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