9DNE

Pseudosymmetric protein nanocage GI9-F7 (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb9DNE/pdb
• EM Map EMD-47038: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-17 Released: 2024-12-18 
• Deposition Author(s): Park, Y.J., Dowling, Q.M., King, N.P., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
• 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: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Hierarchical design of pseudosymmetric protein nanocages

Dowling, Q.M., Park, Y.-J., Fries, C.N., Gerstenmaier, N.C., Ols, S., Yang, E.C., Wargacki, A.J., Dosey, A., Hsia, Y., Ravichandran, R., Walkey, C.D., Burrell, A.L., Veesler, D., Baker, D., King, N.P.

(2024) Nature 

• DOI: https://doi.org/10.1038/s41586-024-08360-6

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 9-mer - A9 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 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: 209.93 kDa 
• Atom Count: 11,436 
• Modelled Residue Count: 1,827 
• Deposited Residue Count: 1,935 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudosymmetric protein nanocage GI9-F7 A chain	A [auth D], C [auth A], H	225	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudosymmetric protein nanocage GI9-F7 C chain	B [auth C], E, G	215	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudosymmetric protein nanocage GI9-F7 B chain	D [auth B], F, I	205	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 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: 2024-12-18 
Deposition Author(s): Park, Y.J., Dowling, Q.M., King, N.P., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158186

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release