Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 109.24 kDa 
• Atom Count: 7,377 
• Modelled Residue Count: 933 
• Deposited Residue Count: 975 
• Unique protein chains: 4

 8HC6

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB9-258 Fab, focused refinement of Fab region

• PDB DOI: 10.2210/pdb8HC6/pdb
• EM Map EMD-34653: 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: 2022-11-01 Released: 2023-01-25 
• Deposition Author(s): Liu, B., Gao, X., Chen, Q., Li, Z., Su, M., He, J., Xiong, X.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SARS-CoV-2 breakthrough infections induce somatically hypermutated broadly neutralizing antibodies against heterologous variants

Yu, H., Liu, B., Zhang, Y., Gao, X., Wang, Q., Xiang, H., Peng, X., Xie, C., Wang, Y., Hu, P., Shi, J., Shi, Q., Zheng, P., Feng, C., Tang, G., Liu, X., Guo, L., Lin, X., Li, J., Liu, C., Huang, Y., Yang, N., Chen, Q., Li, Z., Su, M., Yan, Q., Pei, R., Chen, X., Liu, L., Hu, F., Liang, D., Ke, B., Ke, C., Li, F., He, J., Wang, M., Chen, L., Xiong, X., Tang, X.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth C]	267	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 16  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
Heavy chain of YB9-258 Fab	B [auth H]	220	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of YB9-258	C [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	D [auth B]	273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 3  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth C], F [auth C], G [auth B], H [auth B], I [auth B], J [auth B], K [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: 4.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Liu, B., Gao, X., Chen, Q., Li, Z., Su, M., He, J., Xiong, X.

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Funding Organization	Location	Grant Number
Other government		EKPG21-06
Other government		2021A1515011289
Other government		GRMH-GL

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release