4JGY

Crystal structure of human coxsackievirus A16 uncoating intermediate (space group P4232)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Picornavirus uncoating intermediate captured in atomic detail.

Ren, J.Wang, X.Hu, Z.Gao, Q.Sun, Y.Li, X.Porta, C.Walter, T.S.Gilbert, R.J.Zhao, Y.Axford, D.Williams, M.McAuley, K.Rowlands, D.J.Yin, W.Wang, J.Stuart, D.I.Rao, Z.Fry, E.E.

(2013) Nat Commun 4: 1929-1929

  • DOI: https://doi.org/10.1038/ncomms2889
  • Primary Citation of Related Structures:  
    4JGY, 4JGZ

  • PubMed Abstract: 

    It remains largely mysterious how the genomes of non-enveloped eukaryotic viruses are transferred across a membrane into the host cell. Picornaviruses are simple models for such viruses, and initiate this uncoating process through particle expansion, which reveals channels through which internal capsid proteins and the viral genome presumably exit the particle, although this has not been clearly seen until now. Here we present the atomic structure of an uncoating intermediate for the major human picornavirus pathogen CAV16, which reveals VP1 partly extruded from the capsid, poised to embed in the host membrane. Together with previous low-resolution results, we are able to propose a detailed hypothesis for the ordered egress of the internal proteins, using two distinct sets of channels through the capsid, and suggest a structural link to the condensed RNA within the particle, which may be involved in triggering RNA release.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, Headington, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein, capsid protein VP1297Coxsackievirus A16Mutation(s): 0 
UniProt
Find proteins for I3W9E1 (Coxsackievirus A16)
Explore I3W9E1 
Go to UniProtKB:  I3W9E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3W9E1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein, capsid protein VP2254Coxsackievirus A16Mutation(s): 0 
UniProt
Find proteins for I3W9E1 (Coxsackievirus A16)
Explore I3W9E1 
Go to UniProtKB:  I3W9E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3W9E1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein, capsid protein VP3242Coxsackievirus A16Mutation(s): 0 
UniProt
Find proteins for I3W9E1 (Coxsackievirus A16)
Explore I3W9E1 
Go to UniProtKB:  I3W9E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3W9E1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 357α = 90
b = 357β = 90
c = 357γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description