6ZCL

Coxsackievirus B3 in complex with capsid binder compound 17

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1038/s42003-021-01779-x
  • Primary Citation of 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.

    • Organizational Affiliation: 

    Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP1269Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
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Go to UniProtKB:  P03313
Entity Groups  
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UniProt GroupP03313
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP2252Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
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Go to UniProtKB:  P03313
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UniProt GroupP03313
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP3237Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Explore P03313 
Go to UniProtKB:  P03313
Entity Groups  
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UniProt GroupP03313
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP468Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Explore P03313 
Go to UniProtKB:  P03313
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03313
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FHK (Subject of Investigation/LOI)
Query on FHK
Download Ideal Coordinates CCD File 
E [auth C]4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid
C21 H14 N2 O6 S
KCHARURJHJMOQX-UHFFFAOYSA-N
MYR
Query on MYR
Download Ideal Coordinates CCD File 
F [auth D]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Academy of FinlandFinland315950
Sigrid Juselius FoundationFinlandNA

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references, Derived calculations