8WPY | pdb_00008wpy

Cryo-EM structure of SARS-CoV-2 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies

• PDB DOI: https://doi.org/10.2210/pdb8WPY/pdb
• EM Map EMD-37726: EMDB EMDataResource

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


• Deposited: 2023-10-10 Released: 2024-10-16 
• Deposition Author(s): Su, C., Qi, J.X., Gao, G.F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Enabling the immune escaped etesevimab fully-armed against SARS-CoV-2 Omicron subvariants including KP.2

Su, C., He, J., Xie, Y., Hu, Y., Li, X., Qiao, S., Liu, P., Huang, M., Zhang, R., Wang, L., Chang, Z., Sun, W., Xu, K., Zhang, J., Cao, L., Han, P., Zhao, X., Qi, J., Wang, Q., Yang, M., Gao, G.F.

(2025) Hlife 3: 132-145

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A4B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 172.53 kDa 
• Atom Count: 8,408 
• Modeled Residue Count: 1,090 
• Deposited Residue Count: 1,578 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 fab heavy chain	A	239	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 fab light chain	B	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CB6 fab mutant heavy chain	C	231	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CB6 fab mutant light chain	D	216	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
S304 fab heavy chain	E [auth H]	232	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
S304 fab light chain	F [auth L]	216	Homo sapiens	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	G [auth R]	229	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth E]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Su, C., Qi, J.X., Gao, G.F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection
• Version 1.2: 2025-07-02
  Changes: Data collection
• Version 1.3: 2025-10-29
  Changes: Data collection, Database references