6ZCK

Coxsackievirus B4 in complex with capsid binder compound 48


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.1 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1271Coxsackievirus B4 (strain E2)Mutation(s): 5 
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2))
Explore Q86887 
Go to UniProtKB:  Q86887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86887
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2252Coxsackievirus B4 (strain E2)Mutation(s): 1 
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2))
Explore Q86887 
Go to UniProtKB:  Q86887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86887
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3238Coxsackievirus B4 (strain E2)Mutation(s): 0 
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2))
Explore Q86887 
Go to UniProtKB:  Q86887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86887
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP469Coxsackievirus B4 (strain E2)Mutation(s): 1 
UniProt
Find proteins for Q86887 (Coxsackievirus B4 (strain E2))
Explore Q86887 
Go to UniProtKB:  Q86887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86887
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QFW (Subject of Investigation/LOI)
Query on QFW

Download Ideal Coordinates CCD File 
E [auth C]4-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid
C20 H19 N O5 S
CXGJVZAHQVOLAT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland315950
Sigrid Juselius FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 2.0: 2022-09-21
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 3.0: 2023-05-31
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Structure summary
  • Version 3.1: 2024-07-10
    Changes: Data collection