4GMP

Crystal structure of enterovirus 71 strain 1095 procapsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 

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This is version 1.2 of the entry. See complete history


Literature

Structures of the procapsid and mature virion of enterovirus 71 strain 1095.

Cifuente, J.O.Lee, H.Yoder, J.D.Shingler, K.L.Carnegie, M.S.Yoder, J.L.Ashley, R.E.Makhov, A.M.Conway, J.F.Hafenstein, S.

(2013) J Virol 87: 7637-7645

  • DOI: https://doi.org/10.1128/JVI.03519-12
  • Primary Citation of Related Structures:  
    4GMP

  • PubMed Abstract: 

    Enterovirus 71 (EV71) is an important emerging human pathogen with a global distribution and presents a disease pattern resembling poliomyelitis with seasonal epidemics that include cases of severe neurological complications, such as acute flaccid paralysis. EV71 is a member of the Picornaviridae family, which consists of icosahedral, nonenveloped, single-stranded RNA viruses. Here we report structures derived from X-ray crystallography and cryoelectron microscopy (cryo-EM) for the 1095 strain of EV71, including a putative precursor in virus assembly, the procapsid, and the mature virus capsid. The cryo-EM map of the procapsid provides new structural information on portions of the capsid proteins VP0 and VP1 that are disordered in the higher-resolution crystal structures. Our structures solved from virus particles in solution are largely in agreement with those from prior X-ray crystallographic studies; however, we observe small but significant structural differences for the 1095 procapsid compared to a structure solved in a previous study (X. Wang, W. Peng, J. Ren, Z. Hu, J. Xu, Z. Lou, X. Li, W. Yin, X. Shen, C. Porta, T. S. Walter, G. Evans, D. Axford, R. Owen, D. J. Rowlands, J. Wang, D. I. Stuart, E. E. Fry, and Z. Rao, Nat. Struct. Mol. Biol. 19:424-429, 2012) for a different strain of EV71. For both EV71 strains, the procapsid is significantly larger in diameter than the mature capsid, unlike in any other picornavirus. Nonetheless, our results demonstrate that picornavirus capsid expansion is possible without RNA encapsidation and that picornavirus assembly may involve an inward radial collapse of the procapsid to yield the native virion.


  • Organizational Affiliation

    Department of Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP0A [auth 0]323Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for E5RPG0 (Human enterovirus 71)
Explore E5RPG0 
Go to UniProtKB:  E5RPG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5RPG0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP1B [auth 1]297Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for Q91D09 (Human enterovirus 71)
Explore Q91D09 
Go to UniProtKB:  Q91D09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91D09
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein VP3C [auth 3]242Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for E5RPG0 (Human enterovirus 71)
Explore E5RPG0 
Go to UniProtKB:  E5RPG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5RPG0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 350.248α = 90
b = 350.248β = 90
c = 350.248γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations