9D9S | pdb_00009d9s

Cryo-EM structure of Human Enterovirus D94 full particle

• PDB DOI: https://doi.org/10.2210/pdb9D9S/pdb
• EM Map EMD-46677: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): enterovirus D94
• Mutation(s): No 


• Deposited: 2024-08-21 Released: 2025-09-03 
• Deposition Author(s): Fu, J., Klose, T., Rossmann, M.R., Kuhn, R., Center for Structural Genomics of Infectious Diseases (CSGID)
• 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: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Human Enterovirus D94

Fu, J., Klose, T., Rossmann, M.R., vanKuppeveld, F.J.M., Kuhn, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 91.32 kDa 
• Atom Count: 6,408 
• Modeled Residue Count: 822 
• Deposited Residue Count: 822 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	298	enterovirus D94	Mutation(s): 0
UniProt
Find proteins for A3QWZ2 (enterovirus D94) Explore A3QWZ2  Go to UniProtKB:  A3QWZ2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	238	enterovirus D94	Mutation(s): 0
UniProt
Find proteins for A3QWZ2 (enterovirus D94) Explore A3QWZ2  Go to UniProtKB:  A3QWZ2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	247	enterovirus D94	Mutation(s): 0
UniProt
Find proteins for A3QWZ2 (enterovirus D94) Explore A3QWZ2  Go to UniProtKB:  A3QWZ2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4	D	39	enterovirus D94	Mutation(s): 0
UniProt
Find proteins for A3QWZ2 (enterovirus D94) Explore A3QWZ2  Go to UniProtKB:  A3QWZ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPH	E [auth A]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Fu, J., Klose, T., Rossmann, M.R., Kuhn, R., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI011219

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release