8G7A

SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb8G7A/pdb
• EM Map EMD-29804: EMDB EMDataResource

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


• Deposited: 2023-02-16 Released: 2024-02-21 
• Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 (local refinement)

Ye, G., Bu, F., Pan, R., Wen, W., Mendoza, A., Spiller, B., Du, L., Perlman, S., Liu, B., Li, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 455.6 kDa 
• Atom Count: 16,237 
• Modelled Residue Count: 2,046 
• Deposited Residue Count: 4,110 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-3	A [auth E], D [auth C], F	136	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B [auth A], C [auth B], E [auth D]	1,234	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth B], H [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089728
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI110700

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary