4QPI

Crystal structure of hepatitis A virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.318 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hepatitis A virus and the origins of picornaviruses.

Wang, X.Ren, J.Gao, Q.Hu, Z.Sun, Y.Li, X.Rowlands, D.J.Yin, W.Wang, J.Stuart, D.I.Rao, Z.Fry, E.E.

(2015) Nature 517: 85-88

  • DOI: 10.1038/nature13806
  • Primary Citation of Related Structures:  
    4QPG, 4QPI

  • PubMed Abstract: 
  • Hepatitis A virus (HAV) remains enigmatic, despite 1.4 million cases worldwide annually. It differs radically from other picornaviruses, existing in an enveloped form and being unusually stable, both genetically and physically, but has proved difficult to study ...

    Hepatitis A virus (HAV) remains enigmatic, despite 1.4 million cases worldwide annually. It differs radically from other picornaviruses, existing in an enveloped form and being unusually stable, both genetically and physically, but has proved difficult to study. Here we report high-resolution X-ray structures for the mature virus and the empty particle. The structures of the two particles are indistinguishable, apart from some disorder on the inside of the empty particle. The full virus contains the small viral protein VP4, whereas the empty particle harbours only the uncleaved precursor, VP0. The smooth particle surface is devoid of depressions that might correspond to receptor-binding sites. Peptide scanning data extend the previously reported VP3 antigenic site, while structure-based predictions suggest further epitopes. HAV contains no pocket factor and can withstand remarkably high temperature and low pH, and empty particles are even more robust than full particles. The virus probably uncoats via a novel mechanism, being assembled differently to other picornaviruses. It utilizes a VP2 'domain swap' characteristic of insect picorna-like viruses, and structure-based phylogenetic analysis places HAV between typical picornaviruses and the insect viruses. The enigmatic properties of HAV may reflect its position as a link between 'modern' picornaviruses and the more 'primitive' precursor insect viruses; for instance, HAV retains the ability to move from cell-to-cell by transcytosis.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1A278Human hepatitis A virusMutation(s): 0 
UniProt
Find proteins for Q8QXR6 (Hepatovirus A)
Explore Q8QXR6 
Go to UniProtKB:  Q8QXR6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP2B222Human hepatitis A virusMutation(s): 0 
EC: 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Explore P08617 
Go to UniProtKB:  P08617
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP3C246Human hepatitis A virusMutation(s): 0 
EC: 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Explore P08617 
Go to UniProtKB:  P08617
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.318 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 291.479α = 90
b = 423.261β = 100.152
c = 314.827γ = 90
Software Package:
Software NamePurpose
GDAdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references
  • Version 1.2: 2015-01-21
    Changes: Database references