RCSB PDB - 3VBR: Crystal structure of formaldehyde treated empty human Enterovirus 71 particle (room temperature)

 3VBR

Crystal structure of formaldehyde treated empty human Enterovirus 71 particle (room temperature)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.

Wang, X.Peng, W.Ren, J.Hu, Z.Xu, J.Lou, Z.Li, X.Yin, W.Shen, X.Porta, C.Walter, T.S.Evans, G.Axford, D.Owen, R.Rowlands, D.J.Wang, J.Stuart, D.I.Fry, E.E.Rao, Z.

(2012) Nat Struct Mol Biol 19: 424-429

  • DOI: https://doi.org/10.1038/nsmb.2255
  • Primary Citation of Related Structures:  
    3VBF, 3VBH, 3VBO, 3VBR, 3VBS, 3VBU

  • PubMed Abstract: 

    Enterovirus 71 (EV71) is a major agent of hand, foot and mouth disease in children that can cause severe central nervous system disease and death. No vaccine or antiviral therapy is available. High-resolution structural analysis of the mature virus and natural empty particles shows that the mature virus is structurally similar to other enteroviruses. In contrast, the empty particles are markedly expanded and resemble elusive enterovirus-uncoating intermediates not previously characterized in atomic detail. Hydrophobic pockets in the EV71 capsid are collapsed in this expanded particle, providing a detailed explanation of the mechanism for receptor-binding triggered virus uncoating. These structures provide a model for enterovirus uncoating in which the VP1 GH loop acts as an adaptor-sensor for cellular receptor attachment, converting heterologous inputs to a generic uncoating mechanism, highlighting new opportunities for therapeutic intervention.


  • Organizational Affiliation

    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome Polyprotein, capsid protein VP1225Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Genome Polyprotein, capsid protein VP0237Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Genome Polyprotein, capsid protein VP3239Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 354.9α = 90
b = 354.9β = 90
c = 354.9γ = 90
Software Package:
Software NamePurpose
GDAdata collection
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: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2012-05-02
    Changes: Database references
  • Version 1.4: 2012-05-09
    Changes: Other
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description