7OJ7

Crystal structure of human coxsackievirus A24v in complex with a pentavalent N-acetylneuraminic acid conjugate

  • Classification: VIRUS
  • Organism(s): Coxsackievirus A24
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-05-14 Released: 2021-10-13 
  • Deposition Author(s): Zocher, G., Stehle, T.
  • Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Education and Research

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Work: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exploring the Effect of Structure-Based Scaffold Hopping on the Inhibition of Coxsackievirus A24v Transduction by Pentavalent N-Acetylneuraminic Acid Conjugates.

Johansson, E.Caraballo, R.Hurdiss, D.L.Mistry, N.Andersson, C.D.Thompson, R.F.Ranson, N.A.Zocher, G.Stehle, T.Arnberg, N.Elofsson, M.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms22168418
  • Primary Citation of Related Structures:  
    7OJ7

  • PubMed Abstract: 

    Coxsackievirus A24 variant (CVA24v) is the primary causative agent of the highly contagious eye infection designated acute hemorrhagic conjunctivitis (AHC). It is solely responsible for two pandemics and several recurring outbreaks of the disease over the last decades, thus affecting millions of individuals throughout the world. To date, no antiviral agents or vaccines are available for combating this disease, and treatment is mainly supportive. CVA24v utilizes Neu5Ac-containing glycans as attachment receptors facilitating entry into host cells. We have previously reported that pentavalent Neu5Ac conjugates based on a glucose-scaffold inhibit CVA24v infection of human corneal epithelial cells. In this study, we report on the design and synthesis of scaffold-replaced pentavalent Neu5Ac conjugates and their effect on CVA24v cell transduction and the use of cryogenic electron microscopy (cryo-EM) to study the binding of these multivalent conjugates to CVA24v. The results presented here provide insights into the development of Neu5Ac-based inhibitors of CVA24v and, most significantly, the first application of cryo-EM to study the binding of a multivalent ligand to a lectin.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, SE90187 Umeå, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1A [auth 111]305Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2B [auth 222]271Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3C [auth 333]240Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP4D [auth 444]69Coxsackievirus A24Mutation(s): 0 
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24)
Explore V9VEF3 
Go to UniProtKB:  V9VEF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VEF3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0H0
Query on 0H0

Download Ideal Coordinates CCD File 
K [auth 111]Carbohydrate component from a pentavalent N-acetylneuraminic acid conjugate
C15 H27 N O9
HDYHZAZYSDVKLZ-FSTWUICMSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth 111],
F [auth 111],
G [auth 111]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth 111]
I [auth 111]
J [auth 111]
L [auth 222]
M [auth 222]
H [auth 111],
I [auth 111],
J [auth 111],
L [auth 222],
M [auth 222],
N [auth 222],
O [auth 333]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Work: 0.158 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 305.52α = 90
b = 365.55β = 90
c = 366.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFOR2327
German Federal Ministry for Education and ResearchGermanyBW-Stiftung - Glykobiologie

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description