9Y5Y
Structure of the Omicron Spike RBD bound by the monobody s19382 (local refinement from dimerized Spike protein ECDs)
Summary for 9Y5Y
| Entry DOI | 10.2210/pdb9y5y/pdb |
| EMDB information | 72524 |
| Descriptor | Spike protein S1, Monobody s19382 (2 entities in total) |
| Functional Keywords | inhibitor, complex, viral spike protein, monobody, antiviral protein, antiviral protein-viral protein complex, antiviral protein/viral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 More |
| Total number of polymer chains | 12 |
| Total formula weight | 167645.92 |
| Authors | Noland, C.L.,Perez, C.P.,Huang, P. (deposition date: 2025-09-05, release date: 2025-11-12, Last modification date: 2025-12-17) |
| Primary citation | Perez, C.P.,DelRosso, N.V.,Noland, C.L.,Parekh, U.,Choe, C.A.,Eguchi, R.R.,Wen, Q.,Fordyce, P.M.,Huang, P.S. ADAPT-M: A workflow for rapid, quantitative in vitro measurements of enriched protein libraries. Biorxiv, 2025 Cited by PubMed Abstract: Protein-protein interactions underpin most cellular interactions, and engineered binders present powerful tools for probing biology and developing novel therapeutics. One bottleneck in binder generation is the scalable, quantitative characterization of these interactions. We present ADAPT-M (ffinity etermination by daptation of roein binders for icrofluidics), a streamlined workflow that connects yeast surface display (YSD) with affinity and kinetic measurements using the high-throughput STAMMPPING microfluidic platform. ADAPT-M quantifies s and dissociation kinetic parameters for hundreds of enriched protein variants in under one week without requiring hands-on protein purification. We applied ADAPT-M to a computationally designed library targeting the SARS-CoV-2 Omicron BA.1 receptor binding domain, successfully recovering and measuring s for most highly enriched YSD variants. Measurements correlate strongly with biolayer interferometry and yeast titration assays. ADAPT-M further enabled selection of lead candidates for structural and mutational analysis, which revealed designed paratopes were preserved despite binding to off-target epitopes. By bridging YSD screening and validation, ADAPT-M accelerates protein binder discovery and supports data-driven protein engineering. PubMed: 41279512DOI: 10.1101/2025.10.21.683815 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.16 Å) |
Structure validation
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