9Y5Y | pdb_00009y5y

Structure of the Omicron Spike RBD bound by the monobody s19382 (local refinement from dimerized Spike protein ECDs)

• PDB DOI: https://doi.org/10.2210/pdb9Y5Y/pdb
• EM Map EMD-72524: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN/VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-09-05 Released: 2025-11-12 
• Deposition Author(s): Noland, C.L., Perez, C.P., Huang, P.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

ADAPT-M: A workflow for rapid, quantitative in vitro measurements of enriched protein libraries.

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.

(2025) bioRxiv 

• PubMed: 41279512 
• DOI: https://doi.org/10.1101/2025.10.21.683815
• Primary Citation of Related Structures:  
  9Y5Y


• 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 ( A ffinity D etermination by A daptation of P ro T ein binders for M icrofluidics), a streamlined workflow that connects yeast surface display (YSD) with in vitro affinity and kinetic measurements using the high-throughput STAMMPPING microfluidic platform. ADAPT-M quantifies K _d 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 K _d 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 in vitro validation, ADAPT-M accelerates protein binder discovery and supports data-driven protein engineering.

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Organizational Affiliation: 
• Biophysics Program, Stanford University, Stanford, CA, USA.
Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA, USA.
Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Department of Biochemistry, Stanford University, Stanford, CA, USA.
Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA.
Chan Zuckerberg Biohub, San Francisco, CA, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A8B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 167.65 kDa 
• Atom Count: 11,824 
• Modeled Residue Count: 1,490 
• Deposited Residue Count: 1,492 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, C, E, G	195	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monobody s19382	B, D, F, H, I, J, K, L	89	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Noland, C.L., Perez, C.P., Huang, P.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 1.1: 2025-12-17
  Changes: Data collection, Database references