8HC6

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

• PDB DOI: https://doi.org/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 

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

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 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

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
  
• Version 1.1: 2023-05-03
  Changes: Database references