8WYJ

The global map of Omicron Subvariants Spike with two antibodies

• PDB DOI: https://doi.org/10.2210/pdb8WYJ/pdb
• EM Map EMD-37930: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-10-31 Released: 2024-11-13 
• Deposition Author(s): Yan, R.H., Wang, A.J., Yang, H.N.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The global map of Omicron Subvariants Spike with two antibodies

Yan, R.H., Wang, A.J., Yang, H.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 15-mer - A3B3C3D3E3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 15-mer - A12B3 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3D3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3D3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 524.08 kDa 
• Atom Count: 34,491 
• Modelled Residue Count: 4,476 
• Deposited Residue Count: 4,755 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,123	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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
SA55-HC	D [auth Q], H [auth D], L [auth H]	125	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S309-HC	E [auth S], I [auth E], M [auth I]	127	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SA55_KC	F [auth R], J [auth F], N [auth J]	106	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
S309-KC	G [auth T], K [auth G], O [auth K]	104	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 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: 2024-11-13 
Deposition Author(s): Yan, R.H., Wang, A.J., Yang, H.N.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection