Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B2 Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 450.29 kDa 
• Atom Count: 22,566 
• Modelled Residue Count: 2,878 
• Deposited Residue Count: 4,062 
• Unique protein chains: 3

 8D0Z

S728-1157 IgG in complex with SARS-CoV-2-6P-Mut7 Spike protein (focused refinement)

• PDB DOI:  https://doi.org/10.2210/pdb8D0Z/pdb
• EM Map EMD-27113: EMDB EMDataResource

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


• Deposited: 2022-05-26 Released: 2023-03-22 
• Deposition Author(s): Ozorowski, G., Torres, J.L., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants.

Changrob, S., Halfmann, P.J., Liu, H., Torres, J.L., McGrath, J.J.C., Ozorowski, G., Li, L., Wilbanks, G.D., Kuroda, M., Maemura, T., Huang, M., Zheng, N.Y., Turner, H.L., Erickson, S.A., Fu, Y., Yasuhara, A., Singh, G., Monahan, B., Mauldin, J., Srivastava, K., Simon, V., Krammer, F., Sather, D.N., Ward, A.B., Wilson, I.A., Kawaoka, Y., Wilson, P.C.

(2023) J Clin Invest 133

• PubMed: 36862518 
• DOI: https://doi.org/10.1172/JCI166844
• Primary Citation of Related Structures:  
  8D0Z


• PubMed Abstract: 
  

The rapid evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identified S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) that was derived from an individual previously infected with wildtype SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrated broad cross-neutralization of all dominant variants including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1/XBB). Furthermore, S728-1157 protected hamsters against in vivo challenges with wildtype, Delta, and BA.1 viruses. Structural analysis showed that this antibody targets a class 1/RBS-A epitope in the receptor binding domain (RBD) via multiple hydrophobic and polar interactions with its heavy chain complementarity determining region region 3 (CDR-H3), in addition to common motifs in CDR-H1/CDR-H2 of class 1/RBS-A antibodies. Importantly, this epitope was more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared to diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential, and may inform target-driven vaccine design against future SARS-CoV-2 variants.

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Organizational Affiliation: 

Department of Pediatrics, Weil Cornell Medical College, New York, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth C], B [auth A], C [auth B]	1,280	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 11  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
S728-1157 Fab heavy chain variable region	D [auth H]	118	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S728-1157 Fab light chain variable region	E [auth L]	104	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth C], G [auth C], H [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	Coot	0.9.6
MODEL REFINEMENT	Rosetta
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Ozorowski, G., Torres, J.L., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-00492

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-05-03
  Changes: Database references