9ML8 image
Deposition Date 2024-12-18
Release Date 2025-06-04
Last Version Date 2025-06-04
Entry Detail
PDB ID:
9ML8
Title:
Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.24
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
C 1 2 1
Macromolecular Entities
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:M8b-B1 heavy chain
Chain IDs:E, G (auth: H), I (auth: M), K (auth: P)
Chain Length:235
Number of Molecules:4
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:M8b-B1 light chain
Chain IDs:F, H (auth: L), J (auth: N), L (auth: Q)
Chain Length:217
Number of Molecules:4
Biological Source:Oryctolagus cuniculus
Ligand Molecules
Primary Citation
Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA 122 e2501637122 e2501637122 (2025)
PMID: 40402246 DOI: 10.1073/pnas.2501637122

Abstact

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike-antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

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Primary Citation of related structures