9C8F | pdb_00009c8f

Cryo-EM Structure of EV-D68 B3 A-Particle

• PDB DOI: https://doi.org/10.2210/pdb9C8F/pdb
• EM Map EMD-45303: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): enterovirus D68
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-06-12 Released: 2025-05-21 
• Deposition Author(s): Cheng, J., Krug, P.W., Lei, H., Moss, D.L., Huang, R., Lang, Z.C., Morton, A.J., Shen, C., Pierson, T.C., Zhou, T., Ruckwardt, T.J., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structures of EV-D68 Vaccine Candidates - Virus-like Particle and Inactivated Virus Particle

Cheng, J., Krug, P.W., Lei, H., Moss, D.L., Huang, R., Lang, Z.C., Morton, A.J., Shen, C., Pierson, T.C., Zhou, T., Ruckwardt, T.J., Kwong, P.D.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 180-mer - A60B60C60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 180-mer - A120B60 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 87.53 kDa 
• Atom Count: 5,541 
• Modeled Residue Count: 708 
• Deposited Residue Count: 790 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	295	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A4D5YIF3 (Human enterovirus D68) Explore A0A4D5YIF3  Go to UniProtKB:  A0A4D5YIF3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	248	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A890CN88 (Human enterovirus D68) Explore A0A890CN88  Go to UniProtKB:  A0A890CN88

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	247	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for A0A5C0Q0H5 (Human enterovirus D68) Explore A0A5C0Q0H5  Go to UniProtKB:  A0A5C0Q0H5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 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: 2025-05-21 
Deposition Author(s): Cheng, J., Krug, P.W., Lei, H., Moss, D.L., Huang, R., Lang, Z.C., Morton, A.J., Shen, C., Pierson, T.C., Zhou, T., Ruckwardt, T.J., Kwong, P.D.

---

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

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release