5C8C

Crystal structure of recombinant coxsackievirus A16 capsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

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This is version 1.3 of the entry. See complete history


Literature

Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications for Particle Expansion, Receptor Binding, and Immunogenicity.

Ren, J.Wang, X.Zhu, L.Hu, Z.Gao, Q.Yang, P.Li, X.Wang, J.Shen, X.Fry, E.E.Rao, Z.Stuart, D.I.

(2015) J Virol 89: 10500-10511

  • DOI: https://doi.org/10.1128/JVI.01102-15
  • Primary Citation of Related Structures:  
    5C4W, 5C8C, 5C9A

  • PubMed Abstract: 

    Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) are the primary causes of the epidemics of hand-foot-and-mouth disease (HFMD) that affect more than a million children in China each year and lead to hundreds of deaths. Although there has been progress with vaccines for EV71, the development of a CVA16 vaccine has proved more challenging, and the EV71 vaccine does not give useful cross-protection, despite the capsid proteins of the two viruses sharing about 80% sequence identity. The structural details of the expanded forms of the capsids, which possess nonnative antigenicity, are now well understood, but high resolution information for the native antigenic form of CVA16 has been missing. Here, we remedy this with high resolution X-ray structures of both mature and natural empty CVA16 particles and also of empty recombinant viruslike particles of CVA16 produced in insect cells, a potential vaccine antigen. All three structures are unexpanded native particles and antigenically identical. The recombinant particles have recruited a lipid moiety to stabilize the native antigenic state that is different from the one used in a natural virus infection. As expected, the mature CVA16 virus is similar to EV71; however, structural and immunogenic comparisons highlight differences that may have implications for vaccine production. Hand-foot-and-mouth disease is a serious public health threat to children in Asian-Pacific countries, resulting in millions of cases. EV71 and CVA16 are the two dominant causative agents of the disease that, while usually mild, can cause severe neurological complications, leading to hundreds of deaths. EV71 vaccines do not provide protection against CVA16. A CVA16 vaccine or bivalent EV71/CVA16 vaccine is therefore urgently needed. We report atomic structures for the mature CVA16 virus, a natural empty particle, and a recombinant CVA16 virus-like particle that does not contain the viral genome. All three particles have similar structures and identical antigenicity. The recombinant particles, produced in insect cells (a system suitable for making vaccine antigen), are stabilized by recruiting from the insect cells a small molecule that is different from that used by the virus in a normal infection. We present structural and immunogenic comparisons with EV71 to facilitate structure-based drug design and vaccine development.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1297Coxsackievirus A16 (strain Tainan/5079/98)Mutation(s): 0 
UniProt
Find proteins for Q9QF31 (Coxsackievirus A16 (strain Tainan/5079/98))
Explore Q9QF31 
Go to UniProtKB:  Q9QF31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QF31
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP0323Coxsackievirus A16 (strain Tainan/5079/98)Mutation(s): 0 
UniProt
Find proteins for Q9QF31 (Coxsackievirus A16 (strain Tainan/5079/98))
Explore Q9QF31 
Go to UniProtKB:  Q9QF31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QF31
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP3242Coxsackievirus A16 (strain Tainan/5079/98)Mutation(s): 0 
UniProt
Find proteins for Q9QF31 (Coxsackievirus A16 (strain Tainan/5079/98))
Explore Q9QF31 
Go to UniProtKB:  Q9QF31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QF31
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 347.9α = 90
b = 347.9β = 90
c = 347.9γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations