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 

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:  

  • 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 difficu ...

    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

    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A
278Hepatovirus AMutation(s): 0 
Gene Names: VP1
Find proteins for Q8QXR6 (Hepatovirus A)
Go to UniProtKB:  Q8QXR6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
B
222Human hepatitis A virus genotype IB (isolate HM175)Mutation(s): 0 
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Go to UniProtKB:  P08617
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3
C
246Human hepatitis A virus genotype IB (isolate HM175)Mutation(s): 0 
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Go to UniProtKB:  P08617
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.318 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 291.479α = 90.00
b = 423.261β = 100.15
c = 314.827γ = 90.00
Software Package:
Software NamePurpose
GDAdata collection
CNSrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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