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Structure paper

TitleCross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 21, Page e2501637122, Year 2025
Publish dateMay 27, 2025
AuthorsChengcheng Fan / Jennifer R Keeffe / Kathryn E Malecek / Alexander A Cohen / Anthony P West / Viren A Baharani / Annie V Rorick / Han Gao / Priyanthi N P Gnanapragasam / Semi Rho / Jaasiel Alvarez / Luisa N Segovia / Theodora Hatziioannou / Paul D Bieniasz / Pamela J Bjorkman /
PubMed AbstractBroad 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) ...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.
External linksProc Natl Acad Sci U S A / PubMed:40402246
MethodsEM (single particle) / X-ray diffraction
Resolution2.4 - 3.5 Å
Structure data

48347

9ml4

EMDB-48347, PDB-9ml4:
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-A10 Fab
Method: EM (single particle) / Resolution: 3.3 Å

48348

9ml5

EMDB-48348, PDB-9ml5:
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 Fab
Method: EM (single particle) / Resolution: 3.4 Å

48349

9ml6

EMDB-48349, PDB-9ml6:
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C9 Fab
Method: EM (single particle) / Resolution: 3.5 Å

48350

9ml7

EMDB-48350, PDB-9ml7:
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C10 Fab
Method: EM (single particle) / Resolution: 3.2 Å

PDB-9ml8:
Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-9ml9:
Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.59 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

Source
  • severe acute respiratory syndrome coronavirus 2
  • oryctolagus cuniculus (rabbit)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / immune system / neutralizing antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex / VIRAL PROTEIN-IMMUNE SYSTEM complex

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