7EAI | pdb_00007eai

Echovirus3 empty compacted particle

• PDB DOI: https://doi.org/10.2210/pdb7EAI/pdb
• EM Map EMD-31044: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Echovirus E3
• Mutation(s): No 


• Deposited: 2021-03-07 Released: 2021-07-14 
• Deposition Author(s): Feng, R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for neutralization of an anicteric hepatitis associated echovirus by a potent neutralizing antibody.

Feng, R., Wang, L., Shi, D., Zheng, B., Zhang, L., Hou, H., Xia, D., Cui, L., Wang, X., Xu, S., Wang, K., Zhu, L.

(2021) Cell Discov 7: 35-35

• PubMed: 34035235 
• DOI: https://doi.org/10.1038/s41421-021-00264-3
• Primary Citation Related Structures: 
  7EAH, 7EAI, 7EAJ, 7EAK

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Organizational Affiliation: 
• CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, 100050, China.
National Health Commission of the People's Republic of China, Key laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing, 210009, Jiangsu, China.
Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China.
CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, 100050, China. [e-mail].
CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

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: microscopy

Macromolecule Content 

• Total Structure Weight: 95.97 kDa 
• Atom Count: 5,986 
• Modeled Residue Count: 758 
• Deposited Residue Count: 859 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	292	Echovirus E3	Mutation(s): 0
UniProt
Find proteins for A0A060BKX4 (Echovirus E3) Explore A0A060BKX4  Go to UniProtKB:  A0A060BKX4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP0	B	329	Echovirus E3	Mutation(s): 0
UniProt
Find proteins for A0A0K0LDT3 (Echovirus E3) Explore A0A0K0LDT3  Go to UniProtKB:  A0A0K0LDT3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C	238	Echovirus E3	Mutation(s): 0
UniProt
Find proteins for A0A125RY26 (Echovirus E3) Explore A0A125RY26  Go to UniProtKB:  A0A125RY26

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Feng, R.

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2025-09-17
  Changes: Advisory, Data collection, Derived calculations