6ZMS | pdb_00006zms

Coxsackievirus B4 strain E2

• PDB DOI: https://doi.org/10.2210/pdb6ZMS/pdb
• EM Map EMD-11300: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Coxsackievirus B4 (strain E2)
• Mutation(s): Yes 


• Deposited: 2020-07-03 Released: 2021-03-17 
• Deposition Author(s): Flatt, J.W., Domanska, A., Butcher, S.J.
• Funding Organization(s): Academy of Finland, Sigrid Juselius Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses.

Flatt, J.W., Domanska, A., Seppala, A.L., Butcher, S.J.

(2021) Commun Biol 4: 250-250

• PubMed: 33637854 
• DOI: https://doi.org/10.1038/s42003-021-01779-x
• Primary Citation Related Structures: 
  6ZCK, 6ZCL, 6ZMS


• PubMed Abstract: 
  

  Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals that prevent virus attachment and entry into host cells. To aid with broad-range drug development, we report here structures of coxsackieviruses B3 and B4 bound to different interprotomer-targeting capsid binders using single-particle cryo-EM. The EM density maps are beyond 3 Å resolution, providing detailed information about interactions in the ligand-binding pocket. Comparative analysis revealed the residues that form a conserved virion-stabilizing network at the interprotomer site, and showed the small molecule properties that allow anchoring in the pocket to inhibit virus disassembly.

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Organizational Affiliation: 
• Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland.
Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland. [e-mail].
Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland. [e-mail].

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.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 92.34 kDa 
• Atom Count: 6,396 
• Modeled Residue Count: 818 
• Deposited Residue Count: 830 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	271	Coxsackievirus B4 (strain E2)	Mutation(s): 5
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2)) Explore Q86887  Go to UniProtKB:  Q86887

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP2	B	252	Coxsackievirus B4 (strain E2)	Mutation(s): 1
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2)) Explore Q86887  Go to UniProtKB:  Q86887

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C	238	Coxsackievirus B4 (strain E2)	Mutation(s): 0
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2)) Explore Q86887  Go to UniProtKB:  Q86887

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D	69	Coxsackievirus B4 (strain E2)	Mutation(s): 1
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2)) Explore Q86887  Go to UniProtKB:  Q86887

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Flatt, J.W., Domanska, A., Butcher, S.J.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	315950
Sigrid Juselius Foundation	Finland	--

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 2.0: 2024-05-01
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary