8CSA

Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 3-RBD-Down conformation (S-GSAS-D614G-K417N-E484K-N501Y)

• PDB DOI: https://doi.org/10.2210/pdb8CSA/pdb
• EM Map EMD-26961: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-05-12 Released: 2022-07-20 
• Deposition Author(s): Gobeil, S., Acharya, P.
• 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: 3.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity

Gobeil, S.M.-C., Janowska, K., McDowell, S., Mansouri, K., Parks, R., Stalls, V., Kopp, M.F., Manne, K., Li, D., Wiehe, K., Saunders, K., Edwards, R.J., Korber, B., Haynes, B.F., Henderson, R.C., Acharya, P.

(2021) Science 

• DOI: https://doi.org/10.1126/science.abi6226

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 427.23 kDa 
• Atom Count: 23,442 
• Modelled Residue Count: 3,003 
• Deposited Residue Count: 3,864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 7  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	UCSF Chimera

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Gobeil, S., Acharya, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI145687

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary